A bacterial ice-binding protein from the Vostok ice core

Bacterial and yeast isolates recovered from a deep Antarctic ice core were screened for proteins with ice-binding activity, an indicator of adaptation to icy environments. A bacterial strain recovered from glacial ice at a depth of 3,519 m, just above the accreted ice from Subglacial Lake Vostok, was found to produce a 54 kDa ice-binding protein (GenBank EU694412) that is similar to ice-binding proteins previously found in sea ice diatoms, a snow mold, and a sea ice bacterium. The protein has the ability to inhibit the recrystallization of ice, a phenotype that has clear advantages for survival in ice.     

Genetic diversity and dispersal of the moss Sarconeurum glaciale on Ross Island, East Antarctica

The extent of genetic variation and dispersal mechanisms were investigated over short distances of 1–100 m, and up to 3 km, by the random amplified polymorphic DNA (RAPD) technique, for the moss Sarconeurum glaciale , at three locations on Ross Island, Antarctica. At Arrival Heights, genetic variation occurred within single colonies, and the relationships between clumps indicated that they were dispersed down small, meltwater drainage channels by water. The genetic similarities between the colonies from Arrival Heights and others from Scott Base and Crater Hill, a few km away, together with the prevailing wind direction and absence of this moss in the intervening snow-covered area, suggested longer-distance dispersal by wind. Overall, the Ross Island samples appeared to form a single, polymorphic population that was distinct from another population at Canada Glacier, 110 km distant. Somatic mutation, rather than immigration of genetically different propagules from elsewhere, appeared to be the most probable cause of genetic variability in these haploid, vegetatively reproducing Antarctic moss populations. Initiation of recolonization of S. glaciale across a dirt track at Arrival Heights was also investigated by RAPDs, to investigate how regrowth of mosses in disturbed areas occurred in the extreme environment of Antarctica.     

Molecular microbial diversity of a soil sample and detection of ammonia oxidizers from Cape Evans, Mcmurdo Dry Valley, Antarctica

The aim of our study was to estimate the uncultured eubacterial diversity of a soil sample collected below a dead seal, Cape Evans, McMurdo, Antarctica by an SSU rDNA gene library approach. Our study by sequencing of clones from SSU rDNA gene library approach revealed high diversity in the soil sample from Antarctica. More than 50% of clones showed homology to Cytophaga-Flavobacterium-Bacteroides group; sequences also belonged to alpha, beta, gamma proteobacteria, Thermus-Deinococcus and high GC gram-positive group; Phylogenetic analysis of the SSU rDNA clones showed the presence of species belonging to Cytophaga spp., Vitellibacter vladivostokensis, Aequorivita lipolytica, Aequorivita crocea, Flavobacterium spp., Flexibacter sp., Subsaxibacter broadyi, Bacteroidetes, Roseobacter sp., Sphingomonas baekryungensis, Nitrosospira sp., Nitrosomonas cryotolerans, Psychrobacter spp., Chromohalobacter sp., Psychrobacter okhotskensis, Psychrobacter fozii, Psychrobacter urativorans, Rubrobacter radiotolerans, Marinobacter sp., Rubrobacteridae, Desulfotomaculum aeronauticum and Deinococcus sp. The presence of ammonia oxidizing bacteria in Antarctica soil was confirmed by the presence of the amoA gene. Phylogenetic analysis revealed grouping of clones with their respective groups.     

Characterization of bacterial diversity to a depth of 1500 m in the Outokumpu deep borehole, Fennoscandian Shield

This paper demonstrates the first microbiological sampling of the Outokumpu deep borehole (2516 m deep) aiming at characterizing the bacterial community composition and diversity of sulphate-reducing bacteria (SRB) in Finnish crystalline bedrock aquifers. Sampling was performed using a 1500-m-long pressure-tight tube that provided 15 subsamples, each corresponding to a 100-m section down the borehole. Microbial density measurements, as well as community fingerprinting with 16S rRNA gene-based denaturing gradient gel electrophoresis, demonstrated that microbial communities in the borehole water varied as a function of sampling depth. In the upper part of the borehole, bacteria affiliated to the family Comamonadaceae dominated the bacterial community. Further down the borehole, bacteria affiliated to the class Firmicutes became more prominent and, according to 16S rRNA gene clone libraries, dominated the bacterial community at 1400-1500 m. In addition, the largest number of bacterial classes was observed at 1400-1500 m. The dsrB genes detected in the upper part of the borehole were more similar to the dsrB genes of cultured SRBs, such as the genus Desulfotomaculum, whereas in the deeper parts of the borehole, the dsrB genes were more closely related to the uncultured bacteria that have been detected earlier in deep earth crust aquifers.     

水基钻井液对诸氏鲻虾虎鱼抗氧化酶的影响

目的 研究我国南海区某海洋钻井水基钻井液对诸氏鲻虾虎鱼抗氧化酶的影响.方法在19.75～158 mg/L浓度下,对3月龄诸氏鲻虾虎鱼染毒,并用试剂盒法测定超氧化物歧化酶（SOD）和过氧化氢酶（CAT）的活性.结果 SOD对水基钻井液的毒性暴露不太敏感,在染毒第1天只有最低浓度组受到一定程度的抑制,染毒第2 天各浓度组酶活性均受到一定程度的诱导（12.4%～25.5%）,这种诱导作用在第4天即有所减弱,之后酶活性的变化变缓.CAT则对水基钻井液表现出较强的敏感性.染毒第1 天,各组酶活性均受到明显的诱导,并且各组酶活性表现出明显的浓度效应关系.最高浓度组酶活性最大诱导率达到97%（P＆gt;0.05）.随后虾虎鱼CAT酶活性逐渐下降,第7 天,各染毒组酶活性的抑制率达到58.4%～89.1%.结论 CAT在中毒反应中表现出了敏感性,具备了作为生物标志物的重要条件,有望在今后的实际应用中发挥作用.     

Hydrocarbon contamination changes the bacterial diversity of soil from around Scott Base, Antarctica

A combination of culture-independent and culturing methods was used to determine the impacts of hydrocarbon contamination on the diversity of bacterial communities in coastal soil from Ross Island, Antarctica. While numbers of culturable aerobic heterotrophic microbes were 1-2 orders of magnitude higher in the hydrocarbon-contaminated soil than control soil, the populations were less diverse. Members of the divisions Fibrobacter/Acidobacterium, Cytophaga/Flavobacterium/Bacteroides, Deinococcus/Thermus, and Low G+C gram positive occurred almost exclusively in control soils whereas the contaminated soils were dominated by Proteobacteria; specifically, members of the genera Pseudomonas, Sphingomonas and Variovorax, some of which degrade hydrocarbons. Members of the Actinobacteria were found in both soils.     

Bathymetric distribution of fossil foraminifera within marine sediment cores from the eastern part of Lützow-Holm Bay, East Antarctica, and its paleoceanographic implications

Faunal analysis of fossil foraminifera from marine gravity and piston cores collected by the Japanese Antarctic Research Expeditions (1981 and 1992) is used to estimate the impact of the latest Quaternary paleoceanography on coastal environments of the eastern part of Lützow-Holm Bay, East Antarctica.Accelerator Mass Spectrometry (AMS) carbon-14 ages produced from sedimentary organic carbon were less than 16 ka (non-corrected). Detailed correlation among submarine cores and Holocene elevated marine deposits exposed on the eastern shore of the embayment is difficult due to the indefinite reservoir correction value for marine organic matter and to upward-increasing abnormal ages for some cores.A local carbonate dissolution level can be delineated around the present depth of 300–400 m or shallower in the eastern part of Lützow-Holm Bay during the Holocene, based on distributional trends of arenaceous, calcareous benthic, and planktonic foraminifera recognized within a depth less than 600 m. Downcore recovery of calcareous foraminifera containing Bulimina aculeata from two cores obtained in a drowned glacial trough deeper than 600 m situated far beyond the dissolution depth of CaCO₃ indicates the incursion of warm, high-nutrient, and CaCO₃-saturated Circumpolar Deep Water (CDW) from the offshore area along the trough toward the southeastern coast of Lützow-Holm Bay during the Holocene. The intrusion of CDW impacted on the marine environments of the southeastern coast, thereby contributing to peripheral retreat of the ice sheet as well as increasing calcareous benthic foraminiferal productivity along the southeastern coast of Lützow-Holm Bay.     

Broadscale patterns in the distribution of aquatic and terrestrial vegetation at three ice-free regions on Ross Island,Antarctica

Distribution patterns are presented for selected aquatic algae, and terrestrial algae, mosses and lichens, at three large, coastal ice-free regions on Ross Island. Each region is unique in certain aspects of its vegetation. The variation in areal and quantitative occurrence of different components of the vegetation in diverse ponds and streams, and over exposed ground surfaces, is related to the levels of marine salts in the environment, fertilisation by birds, water availability, substratum type and degree of exposure. A comparison is made with other antarctic, coastal, ice-free regions where similar broadscale patterns have been recognised.     

A gas vesiculate planktonic strain of the purple non-sulfur bacterium Rhodoferax antarcticus isolated from Lake Fryxell, Dry Valleys, Antarctica

A moderately psychrophilic purple non-sulfur bacterium, Rhodoferax antarcticus strain Fryx1, is described. Strain Fryx1 was isolated from the water column under the ice of the permanently frozen Lake Fryxell, Antarctica. Cells of Fryx1 are long thin rods and contain gas vesicles, the first report of such structures in purple non-sulfur bacteria. Gas vesicles are clustered at 2–4 sites per cell. Surprisingly, the 16S rRNA gene sequence of strain Fryx1 is nearly identical to that of Rfx. antarcticus strain AB, a short, vibrio-shaped phototroph isolated from an Antarctic microbial mat. Although showing physiological parallels, strains AB and Fryx1 differ distinctly in their morphology and absorption spectra. DNA–DNA hybridization shows that the genomes of strains AB and Fryx1 are highly related, yet distinct. We conclude that although strains AB and Fryx1 may indeed be the same species, their ecologies are quite different. Unlike strain AB, strain Fryx1 has adapted to a planktonic existence in the nearly freezing water column of Lake Fryxell.Dedicated to Prof. Dr. Hans Günter Schlegel on the occasion of his 80th birthday.     

Molecular analysis of fungal diversity associated with three bryophyte species in the Fildes Region, King George Island, maritime Antarctica

The fungal communities associated with three bryophytes species (the liverwort Barbilophozia hatcheri, the mosses Chorisodontium aciphyllum and Sanionia uncinata) in the Fildes Region, King George Island, maritime Antarctica, were studied using clone library analysis. Fungal communities showed low diversity; the 680 clones belonged to 93 OTUs. Of these, 78 belonged to the phylum Ascomycota, 13 to the phylum Basidiomycota, 1 to the phylum Zygomycota, and 1 to an unknown phylum. Among the OTUs, the most common orders in the Ascomycota were Helotiales (42 OTUs) and Chaetothyriales (14 OTUs) and the most common orders in the Basidiomycota were Sebacinales (3 OTUs) and Platygloeales (3 OTUs). Most OTUs clustered within clades that contained phylotypes identified from samples in Antarctic or Arctic ecosystems or from bryophytes in other ecosystems. In addition, we found that host-related factor may shape the fungal communities associated with bryophytes in this region. This is the first systematic study of the fungal community in Antarctic bryophytes to be performed using culture-independent method and the results may improve understanding of the endophytic fungal evolution and ecology in the Antarctic ecosystem.     

Molecular analysis of prokaryotic diversity in the deep subsurface of the former Homestake gold mine,South Dakota,USA

A culture-independent molecular phylogenetic analysis was carried out to study the prokaryotic diversity in two soil samples collected from the subsurface (1.34 km depth) of the former Homestake gold mine, Lead, South Dakota, USA at two sites, the Ross shaft and number 6 Winze. Microbial community analyses were performed by cloning and sequencing of 16S rRNA genes retrieved directly from soil samples. Geochemical characterization of soils revealed high amount of toxic metals such as As, Cd, Co, Cr, Cu, Ni, Pb, Zn, and U at both the sites. Phylogenetic analyses showed that soil samples were predominantly composed of phylotypes related to phylum Proteobacteria. Other phyla detected in libraries were Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Chlorobi, Firmicutes, Gemmatimonadetes, Nitrospirae, Planctomycetes, Verrucomicrobia, and candidate divisions OP10 and TM7. The majority (>95%) of the phylotypes retrieved in the libraries were most closely related to environmental sequences from yet-uncultured bacteria representing a hitherto unidentified diversity. The archaeal communities at both the sites exhibited lower diversity and were most closely affiliated to uncultivated species within the Crenarchaeota. Results showed the existence of diverse microbial populations in deep subsurface environment of the Homestake gold mine. Statistical analyses demonstrated that each site harbored phylogenetically distinct microbial populations that were more diverse at Ross site compare to winze site.     

Microeukaryotic diversity in marine environments,an analysis of surface layer sediments from the East Sea

Molecular techniques, based on clone library of 18S rRNA gene, were employed to ascertain the diversity of microeukaryotic organisms in sediments from the East Sea. A total of 261 clones were recovered from surface sediments. Most of the clone sequences (90%) were affiliated with protists, dominated by Ciliates (18%) and Dinoflagellates (19%) of Alveolates, phototrophic Stramenopiles (11%), and Cercozoa (20%). Many of the clones were related to uncultivated eukaryotes clones retrieved from anoxic environments with several highly divergent 18S rRNA gene sequences. However, no clones were related to cultivated obligate anaerobic protists. Protistan communities between subsurface layers of 1 and 9 cm shared 23% of total phylotypes which comprised 64% of total clones retrieved. Analysis of diversity indices and rarefaction curve showed that the protistan community within the 1 cm layer exhibited higher diversity than the 9 cm layer. Our results imply that diverse protists remain to be uncovered within marine benthic environments.     

Depth-related changes to density,diversity and structure of benthic megafaunal assemblages in the Fimbul ice shelf region,Weddell Sea,Antarctica

The depth-related patterns in the benthic megafauna of the NE Weddell Sea shelf at the edge of the Fimbul Ice Shelf were investigated at seven sites using towed camera platform photographs. Megafaunal density decreased with depth from 77,939 ha⁻¹ at 245 m to 8,895 ha⁻¹ at 510 m. While diversity was variable, with H′ ranging between 1.34 and 2.28, there were no depth related patterns. Multivariate analyses revealed two distinct assemblages; a shallow assemblage with dense patches of suspension feeders in undisturbed areas and a deep assemblage where these were not present. Disturbance from icebergs explained many observed patterns in faunal distribution. In shallow waters probable effects of disturbance were observed as changes in successional stages; in deeper waters changes in habitat as a result of past disturbance explained faunal distributions. In deeper areas ice ploughing created a mosaic landscape of fine and coarse sediments. Total megafaunal density was highest in areas of coarse sediment (up to 2.9 higher than in finer sediment areas) but diversity was highest in intermediate areas (H′ = 2.35).     

Variation with depth of the abundance,diversity and pigmentation of culturable bacteria in a deep ice core from the Yuzhufeng Glacier,Tibetan Plateau

It has been suggested that the cryosphere is a new biome uniquely dominated by microorganisms, although the ecological characteristics of these cold-adapted bacteria are not well understood. We investigated the vertical variation with depth of the proportion of pigmented bacteria recovered from an ice core drilled in the Yuzhufeng Glacier, Tibetan Plateau. A total of 25,449 colonies were obtained from 1250 ice core sections. Colonies grew on only one-third of the inoculated Petri dishes, indicating that although the ice core harbored abundant culturable bacteria, bacteria could not be isolated from every section. Four phyla and 19 genera were obtained; Proteobacteria formed the dominant cluster, followed by Actinobacteria, Bacteroidetes and Firmicutes. The proportion of pigmented bacteria increased with depth from 79 to 95% and yellow-colored colonies predominated throughout the ice core, making up 47% of all the colonies. Pigments including α- and β-carotene, diatoxanthin, peridinin, zea/lutein, butanoyloxy, fucoxanthin and fucoxanthin were detected in representative colonies with α-carotene being the dominant carotenoid. To the best of our knowledge, this is the highest resolution study of culturable bacteria in a deep ice core reported to date.

     

Methanogen and bacterial diversity and distribution in deep gas hydrate sediments from the Cascadia Margin as revealed by 16S rRNA molecular analysis

The microbial community of a deep (to 234 m below the sea floor) sediment gas hydrate deposit (Cascadia Margin Ocean Drilling Program Site 889/890, Leg 146) was analysed for the first time by molecular genetic techniques. Both bacterial and methanogen diversity were determined by phylogenetic analysis of ribosomal DNA sequences. High molecular mass DNA, indicative of active bacteria, was present in all of the samples. Ribosomal RNA genes were amplified from extracted DNA extracted from sediment using bacteria, and methanogen specific PCR primers, the latter designed in this study. Phylogenetic analysis of approximately 400 bacterial clones demonstrated that 96% were members of the Proteobacteria. These clones were affiliated with the alpha, beta and gamma subdivisions, with Caulobacter (Zymomonas group), Ralstonia and Pseudomonas phylotypes predominating. The methanogen clones were of low diversity and clustered in three sub-groups. Two of these sub-groups (contained 96% of the 400 clones) were closely related to Methanosarcina mazeii, while the third sub-group clustered in the Methanobacteriales. This analysis of a deep sediment gas hydrate environment shows a bacteria and methanogen community of limited diversity and confirms that the gas hydrate zone is biogeochemically active. These results are consistent with the presence of bacterial populations capable of methanogenesis throughout the core, and suggest that the methane hydrate at this site is at least partially biogenic in origin.     

Surface-associated diatoms from marine habitats at Cape Evans,Antarctica, including the first record of living <Emphasis Type="Italic">Eunotogramma marginopunctatum</Emphasis>

The diversity of diatom communities found epiphytically on red macroalgae collected under the sea ice at Cape Evans, Antarctica, was studied microscopically. Comparison of communities along a depth profile showed that species diversity decreased as depth below sea ice increased. Dominant taxa also changed with depth, with Cocconeis fasciolata dominant at 10 and 15 m, Porosira glacialis at 20 m and Eunotogramma marginopunctatum at 25 m. Epiphytic communities were also compared to sympagic and sediment-associated communities collected from a single depth. Species richness was greatest for communities associated with surface sediments while the poorest was found in sympagic, or sea-ice, communities. E. marginopunctatum, previously only described from fossil material, was found associated epiphytically on macroalgae from 20 to 25 m below sea ice.     

Nematodes from saline and freshwater lakes of the Vestfold Hills,East Antarctica,including the description of <Emphasis Type=Italic>Hypodontolaimus antarcticus</Emphasis> sp. n.

The invertebrate fauna of many Antarctic ice-free areas, even those close to permanent research stations, can be poorly known. Here we describe some nematodes from freshwater and saline, marine-derived lakes of the Vestfold Hills, East Antarctica. The freshwater lakes contained the widespread East Antarctic endemic species, Plectus frigophilus Kirjanova, 1958. The saline lakes were inhabited by two recently described species, Halomonhystera halophila Andrássy, 2006 and Halomonhystera continentalis Andrássy, 2006, and by a new species described in this report, Hypodontolaimus antarcticus sp. n. Originally marine but now brackish Highway Lake contained a nematode fauna with both freshwater and marine-derived components. The nematode fauna of Antarctica now consists of 54 named species, 22 of which are found in East Antarctica.     

Phytoplankton dynamics in relation to hydrography, nutrients and zooplankton at the onset of sea ice formation in the eastern Weddell Sea (Antarctica)

The quantitative and qualitative distribution of phytoplankton was investigated along five North–South transects in the eastern Weddell Sea during the transition from late autumn to winter. Relationships with the regional hydrography, progressing sea ice coverage, nutrient distribution and zooplankton are discussed and compared with data from other seasons. To the north of the Antarctic Slope Front (ASF) a remnant temperature minimum layer was found above the primary pycnocline throughout summer. Surface waters had not entirely acquired typical winter characteristics. While temperature was already in the winter range, this was not the case for salinity. Highest biomass of phytoplankton, with the exception of the first transect, was found in the region adjoining the ASF to the north. Absolute chlorophyll a (Chl a) concentrations dropped from 0.35 to 0.19 g l^–1 . Nutrient pools exhibited a replenishing tendency. Ammonium concentrations were high (0.75–2 mol l^–1), indicating extensive heterotrophic activity. The phytoplankton in the ASF region was dominated by nanoflagellates, particularly Phaeocystis spp.. North of the ASF the abundance of diatoms increased, with Fragilariopsis spp., F. cylindrus and Thalassiosira spp. dominating. Community structure varied both due to hydrographical conditions and the advancing ice edge. The phytoplankton assemblage formed during late autumn were very similar to the ones found in early spring. A POC/PON ratio close to Redfield, decreasing POC concentration and a high phaeophytin/Chl a ratio, as well as a high abundance of mesozooplankton indicated that a strong grazing pressure was exerted on the phytoplankton community. A comparison between primary production (PP) in the water column and the sea ice showed a shift of the major portion of PP into the ice during the period of investigation.