DGGE fingerprinting of bacteria in soils from eight ecologically different sites around Casey Station, Antarctica

Advances in research on petroleum biodegradability in soil

With the increased demand for petroleum and petroleum products from all parts of the society, environmental pollution caused by petroleum development and production processes is becoming increasingly serious. Soil pollution caused by petroleum seriously affects environmental quality in addition to human lives and productivity. At present, petroleum in soil is mainly degraded by biological methods. In their natural state, native bacteria in the soil spontaneously degrade petroleum pollutants that enter the soil; however, when the pollution levels increase, the degradation rates decrease, and it is necessary to add nutrients, dissolved oxygen, biosurfactants and other additives to improve the degradation ability of the native bacteria in the soil. The degradation process can also be enhanced by adding exogenous petroleum-degrading bacteria, microbial immobilization technologies, and microbial fuel cell technologies.

Prokaryotic Diversity and Composition of Sediments From Prydz Bay, the Antarctic Peninsula Region, and the Ross Sea, Southern Ocean

The V3–V4 hypervariable regions of the 16S ribosomal RNA gene were analyzed to assess prokaryotic diversity and community compositions within 19 surface sediment samples collected from three different regions (depth: 250–3,548 m) of Prydz Bay, the Antarctic Peninsula region, and the Ross Sea. In our results, we characterized 1,079,709 clean tag sequences representing 43,227 operational taxonomic units (OTUs, 97% similarity). The prokaryotic community distribution exhibited obvious geographical differences, and the sequences formed three distinct clusters according to the samples’ origins. In general, the biodiversity of Prydz Bay was higher than those of the Antarctic Peninsula region and the Ross Sea, and there were similar prokaryotic communities in different geographic locations. The most dominant clades in the prokaryotic communities were Proteobacteria, Bacteroidetes, Thaumarchaeota, Oxyphotobacteria, Deinococcus-Thermus, Firmicutes, Acidobacteria, Fusobacteria, and Planctomycetes, but unique prokaryotic community compositions were found in each of the sampling regions. Our results also demonstrated that the prokaryotic diversity and community distribution were mainly influenced by geographical and physicochemical factors, such as Zn, V, Na, K, water depth, and especially geographical distance (longitude variation of sample location) and Ba ion content. Moreover, geochemical factors such as nutrient contents (TC, P, and Ca) also played important roles in prokaryotic diversity and community distribution. This represents the first report that Ba ion content has an obvious effect on prokaryotic diversity and community distribution in Southern Ocean sediments.

Altitude and fungal diversity influence the structure of Antarctic cryptoendolithic Bacteria communities

Endolithic growth within rocks is a critical adaptation of microbes living in harsh environments where exposure to extreme temperature, radiation, and desiccation limits the predominant life forms, such as in the ice-free regions of Continental Antarctica. The microbial diversity of the endolithic communities in these areas has been sparsely examined. In this work, diversity and composition of bacterial assemblages in the cryptoendolithic lichen-dominated communities of Victoria Land (Continental Antarctica) were explored using a high-throughput metabarcoding approach, targeting the V4 region of 16S rDNA. Rocks were collected in 12 different localities (from 14 different sites), along a gradient ranging from 1000 to 3300 m a.s.l. and at a sea distance ranging from 29 to 96 km. The results indicate Actinobacteria and Proteobacteria are the dominant taxa in all samples and defined a 'core' group of bacterial taxa across all sites. The structure of bacteria communities is correlated with the fungal counterpart and among the environmental parameters considered, altitude was found to influence bacterial biodiversity, while distance from sea had no evident influence.

Antarctic Cryptoendolithic Fungal Communities Are Highly Adapted and Dominated by Lecanoromycetes and Dothideomycetes

Endolithic growth is one of the most spectacular microbial adaptations to extreme environmental constraints and the predominant life-form in the ice-free areas of Continental Antarctica. Although Antarctic endolithic microbial communities are known to host among the most resistant and extreme-adapted organisms, our knowledge on microbial diversity and composition in this peculiar niche is still limited. In this study, we investigated the diversity and structure of the fungal assemblage in the cryptoendolithic communities inhabiting sandstone using a meta-barcoding approach targeting the fungal Internal Transcribed Sequence region 1 (ITS1). Samples were collected from 14 sites in the Victoria Land, along an altitudinal gradient ranging from 1,000 to 3,300 m a.s.l. and from 29 to 96 km distance to coast. Our study revealed a clear dominance of a 'core' group of fungal taxa consistently present across all the samples, mainly composed of lichen-forming and Dothideomycetous fungi. Pareto-Lorenz curves indicated a very high degree of specialization (F0 approximately 95%), suggesting these communities are highly adapted but have limited ability to recover after perturbations. Overall, both fungal community biodiversity and composition did not show any correlation with the considered abiotic parameters, potentially due to strong fluctuations of environmental conditions at local scales.

Bacterial communities and chemical parameters in soils and coastal sediments in response to diesel spills at Carlini Station, Antarctica

A diesel spill occurring at Carlini Station (King George Island (Isla 25 de Mayo), South Shetland Islands) in 2009 started the study of the fate of the hydrocarbons and their effect on the bacterial communities of the Potter Cove ecosystem. Soils and sediments were sampled across the 200-meter long diesel plume towards Potter Cove four and 15months after the spill. The sampling revealed a second fuel leakage from an underground pipeline at the spill site. The hydrocarbon fraction spilt over frozen and snow-covered ground reached the sea and dispersed with the currents. Contrary, diesel that infiltrated unfrozen soil remained detectable for years, and was seeping with ground water towards coastal marine sediments. Structural changes of the bacterial communities as well as hydrocarbon, carbon and nitrogen contents were investigated in sediments in front of the station, two affected terrestrial sites, and a terrestrial non-contaminated reference site. Bacterial communities (16S rRNA gene clone libraries) changed over time in contaminated soils and sediments. At the underground seepage site of highest contamination (5812 to 366μgg^-1_dw hydrocarbons from surface to 90-cm depth), communities were dominated by Actinobacteria (18%) and a betaproteobacterium closely related to Polaromonas naphthalenivorans (40%). At one of the spill sites, affected exclusively at the surface, contamination disappeared within one year. The same bacterial groups were enriched at both contaminated sites. This response at community level suggests that the cold-adapted indigenous microbiota in soils of the West Antarctic Peninsula have a high potential for bioremediation and can support soil cleaning actions in the ecosystem. Intensive monitoring of pollution and site assessment after episodic fuel spills is required for decision-making towards remediation strategies.

Diversity structure of culturable bacteria isolated from the Fildes Peninsula (King George Island, Antarctica): A phylogenetic analysis perspective

It has been proposed that Antarctic environments select microorganisms with unique biochemical adaptations, based on the tenet 'Everything is everywhere, but, the environment selects' by Baas-Becking. However, this is a hypothesis that has not been extensively evaluated. This study evaluated the fundamental prediction contained in this hypothesis-in the sense that species are structured in the landscape according to their local habitats-, using as study model the phylogenetic diversity of the culturable bacteria of Fildes Peninsula (King George Island, Antarctica). Eighty bacterial strains isolated from 10 different locations in the area, were recovered. Based on phylogenetic analysis of 16S rRNA gene sequences, the isolates were grouped into twenty-six phylotypes distributed in three main clades, of which only six are exclusive to Antarctica. Results showed that phylotypes do not group significantly by habitat type; however, local habitat types had phylogenetic signal, which support the phylogenetic niche conservatism hypothesis and not a selective role of the environment like the Baas-Becking hypothesis suggests. We propose that, more than habitat selection resulting in new local adaptations and diversity, local historical colonization and species sorting (i.e. differences in speciation and extinction rates that arise by interaction of species level traits with the environment) play a fundamental role on the culturable bacterial diversity in Antarctica.

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 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.

Biological synthesis of fluorescent nanoparticles by cadmium and tellurite resistant Antarctic bacteria: exploring novel natural nanofactories

Background

Fluorescent nanoparticles or quantum dots (QDs) have been intensely studied for basic and applied research due to their unique size-dependent properties. There is an increasing interest in developing ecofriendly methods to synthesize these nanoparticles since they improve biocompatibility and avoid the generation of toxic byproducts. The use of biological systems, particularly prokaryotes, has emerged as a promising alternative. Recent studies indicate that QDs biosynthesis is related to factors such as cellular redox status and antioxidant defenses. Based on this, the mixture of extreme conditions of Antarctica would allow the development of natural QDs producing bacteria.

Results

In this study we isolated and characterized cadmium and tellurite resistant Antarctic bacteria capable of synthesizing CdS and CdTe QDs when exposed to these oxidizing heavy metals. A time dependent change in fluorescence emission color, moving from green to red, was determined on bacterial cells exposed to metals. Biosynthesis was observed in cells grown at different temperatures and high metal concentrations. Electron microscopy analysis of treated cells revealed nanometric electron-dense elements and structures resembling membrane vesicles mostly associated to periplasmic space. Purified biosynthesized QDs displayed broad absorption and emission spectra characteristic of biogenic Cd nanoparticles.

Conclusions

Our work presents a novel and simple biological approach to produce QDs at room temperature by using heavy metal resistant Antarctic bacteria, highlighting the unique properties of these microorganisms as potent natural producers of nano-scale materials and promising candidates for bioremediation purposes.

Bacterial diversity is strongly associated with historical penguin activity in an Antarctic lake sediment profile

Current penguin activity in Antarctica affects the geochemistry of sediments and their microbial communities; the effects of historical penguin activity are less well understood. Here, bacterial diversity in ornithogenic sediment was investigated using high-throughput pyrosequencing. The relative abundances of dominant phyla were controlled by the amount of historical penguin guano deposition. Significant positive correlations were found between both the bacterial richness and diversity, and the relative penguin number (p < 0.01); this indicated that historical penguin activity drove the vertical distribution of the bacterial communities. The lowest relative abundances of individual phyla corresponded to lowest number of penguin population at 1,800–2,300 yr BP during a drier and colder period; the opposite was observed during a moister and warmer climate (1,400–1,800 yr BP). This study shows that changes in the climate over millennia affected penguin populations and the outcomes of these changes affect the sediment bacterial community today.

Diversity and structure of soil bacterial communities in the Fildes Region (maritime Antarctica) as revealed by 454 pyrosequencing

This study assessed the diversity and composition of bacterial communities in four different soils (human-, penguin-, seal-colony impacted soils and pristine soil) in the Fildes Region (King George Island, Antarctica) using 454 pyrosequencing with bacterial-specific primers targeting the 16S rRNA gene. Proteobacteria, Actinobacteria, Acidobacteria, and Verrucomicrobia were abundant phyla in almost all the soil samples. The four types of soils were significantly different in geochemical properties and bacterial community structure. Thermotogae, Cyanobacteria, Fibrobacteres, Deinococcus-Thermus, and Chlorobi obviously varied in their abundance among the 4 soil types. Considering all the samples together, members of the genera Gaiella, Chloracidobacterium, Nitrospira, Polaromonas, Gemmatimonas, Sphingomonas, and Chthoniobacter were found to predominate, whereas members of the genera Chamaesiphon, Herbaspirillum, Hirschia, Nevskia, Nitrosococcus, Rhodococcus, Rhodomicrobium, and Xanthomonas varied obviously in their abundance among the four soil types. Distance-based redundancy analysis revealed that pH (p < 0.01), phosphate phosphorus (p < 0.01), organic carbon (p < 0.05), and organic nitrogen (p < 0.05) were the most significant factors that correlated with the community distribution of soil bacteria. To our knowledge, this is the first study to explore the soil bacterial communities in human-, penguin-, and seal- colony impacted soils from ice-free areas in maritime Antarctica using high-throughput pyrosequencing.

Denaturing gradient gel electrophoresis fingerprinting of soil bacteria in the vicinity of the Chinese Great Wall Station, King George Island, Antarctica

Bacterial diversity was investigated in soil samples collected from 13 sites around the Great Wall Station, Fildes Peninsula, King George Island, Antarctica, using denaturing gradient gel electrophoresis (DGGE) of 16S rRNA genes. The classes alpha-, beta-, and gamma-Proteobacteria, as well as the phylum Actinobacteria, were found to be the dominant bacteria in the soils around the Great Wall Station. Although the selected samples were not contaminated by oil, a relationship between soil parameters, microbial biodiversity, and human impact was still seen. Sample sites in human impacted areas showed lower bacterial biodiversity (average H' = 2.65) when compared to non-impacted sites (average H' = 3.05). There was no statistically significant correlation between soil bacterial diversity and total organic carbon (TOC), total nitrogen, or total phosphorus contents of the soil. Canonical correlation analysis showed that TOC content was the most important factor determining bacterial community profiles among the measured soil parameters. In conclusion, microbial biodiversity and community characteristics within relatively small scales (1.5 km) were determined as a function of local environment parameters and anthropogenic impact.

The impact of different soil parameters on the community structure of dominant bacteria from nine different soils located on Livingston Island, South Shetland Archipelago, Antarctica

Microorganisms inhabit very different soil habitats in the ice-free areas of Antarctica, playing a major role in nutrient cycling in cold environments. We studied the soil characteristics and the dominant bacterial composition from nine different soil profiles located on Livingston Island (maritime Antarctica). The total carbon (TC) and total nitrogen (TN) values were high for the vegetated soils, decreasing with depth, whereas the values for the mineral soils were generally low. Soil pH was more acidic for moss-covered soils and neutral to alkaline for mineral soils. Numbers of culturable heterotrophic bacteria were higher at vegetated sites, but significant numbers were also detectable in carbon-depleted soils. Patterns of denaturing gradient gel electrophoresis (DGGE) revealed a highly heterogeneous picture throughout the soil profiles. Subsequent sequencing of DGGE bands revealed in total 252 sequences that could be assigned to 114 operational taxonomic units, showing the dominance of members of the Bacteroidetes and Acidobacteria. The results of phospholipid fatty acid analysis showed a lack of unsaturated fatty acids for most of the samples. Samples with a prevalence of unsaturated over saturated fatty acids were restricted to several surface samples. Statistical analysis showed that the dominant soil bacterial community composition is most affected by TC and TN contents and soil physical factors such as grain size and moisture, but not pH.