Subglacial Lake Vostok (Antarctica) Accretion Ice Contains a Diverse Set of Sequences from Aquatic, Marine and Sediment-Inhabiting Bacteria and Eukarya

Lake Vostok, the 7th largest (by volume) and 4th deepest lake on Earth, is covered by more than 3,700 m of ice, making it the largest subglacial lake known. The combination of cold, heat (from possible hydrothermal activity), pressure (from the overriding glacier), limited nutrients and complete darkness presents extreme challenges to life. Here, we report metagenomic/metatranscriptomic sequence analyses from four accretion ice sections from the Vostok 5G ice core. Two sections accreted in the vicinity of an embayment on the southwestern end of the lake, and the other two represented part of the southern main basin. We obtained 3,507 unique gene sequences from concentrates of 500 ml of 0.22 μm-filtered accretion ice meltwater. Taxonomic classifications (to genus and/or species) were possible for 1,623 of the sequences. Species determinations in combination with mRNA gene sequence results allowed deduction of the metabolic pathways represented in the accretion ice and, by extension, in the lake. Approximately 94% of the sequences were from Bacteria and 6% were from Eukarya. Only two sequences were from Archaea. In general, the taxa were similar to organisms previously described from lakes, brackish water, marine environments, soil, glaciers, ice, lake sediments, deep-sea sediments, deep-sea thermal vents, animals and plants. Sequences from aerobic, anaerobic, psychrophilic, thermophilic, halophilic, alkaliphilic, acidophilic, desiccation-resistant, autotrophic and heterotrophic organisms were present, including a number from multicellular eukaryotes. © 2013 Shtarkman et al

Ecology of Subglacial Lake Vostok (Antarctica), Based on Metagenomic/Metatranscriptomic Analyses of Accretion Ice

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The Genomic Contributions of Avian H1N1 Influenza A Viruses to the Evolution of Mammalian Strains

<div><p>Among the influenza A viruses (IAVs) in wild aquatic birds, only H1, H2, and H3 subtypes have caused epidemics in humans. H1N1 viruses of avian origin have also caused 3 of 5 pandemics. To understand the reappearance of H1N1 in the context of pandemic emergence, we investigated whether avian H1N1 IAVs have contributed to the evolution of human, swine, and 2009 pandemic H1N1 IAVs. On the basis of phylogenetic analysis, we concluded that the polymerase gene segments (especially PB2 and PA) circulating in North American avian H1N1 IAVs have been reintroduced to swine multiple times, resulting in different lineages that led to the emergence of the 2009 pandemic H1N1 IAVs. Moreover, the similar topologies of hemagglutinin and nucleoprotein and neuraminidase and matrix gene segments suggest that each surface glycoprotein coevolved with an internal gene segment within the H1N1 subtype. The genotype of avian H1N1 IAVs of Charadriiformes origin isolated in 2009 differs from that of avian H1N1 IAVs of Anseriformes origin. When the antigenic sites in the hemagglutinin of all 31 North American avian H1N1 IAVs were considered, 60%-80% of the amino acids at the antigenic sites were identical to those in 1918 and/or 2009 pandemic H1N1 viruses. Thus, although the pathogenicity of avian H1N1 IAVs could not be inferred from the phylogeny due to the small dataset, the evolutionary process within the H1N1 IAV subtype suggests that the circulation of H1N1 IAVs in wild birds poses a continuous threat for future influenza pandemics in humans.</p></div

Schematic of the evolutionary history among HA, NP, NA and M segments of H1N1 IAVs.

<p>The schematic view is based on the phylogenetic trees of avian, swine, and human origin H1N1 IAVs and the most recent common ancestor (MRCA) for (A) HA and NP gene segments and (B) NA and M gene segments. North American avian (light blue) and 2009 pandemic H1N1 viruses (pink) are highlighted.</p

Evolutionary relatedness of PB2 gene segments of H1N1 IAVs of avian, swine, and human origins isolated from North America and Eurasia.

<p>The taxa are colored based on their host and geography: red-North American avian isolates from the St. Jude repository, light blue-North American avian isolates, purple-Eurasian avian isolates, green- swine isolates from North America, grey- swine isolates from Eurasia (both Eurasian avian-like swine and Eurasian classical swine), dark blue-human isolates from North America; orange- human isolates from Eurasia, and pink- 2009 pandemic isolates. The nodes with spillover avian H1N1 IAVs are denoted with light blue arrows.</p

Percent mortality and pathogenicity in DBA/2J mice infected with various subtypes of avian influenza A viruses (at 10⁶ EID₅₀).

a<p>The survival score was calculated as 0.8× (survival AUC/maximum AUC).</p>b<p>The weight loss score was calculated as 0.2× (weight loss AUC/maximum AUC).</p>c<p>The total pathogenicity score is the sum of the survival and weight loss scores.</p>d<p>Pathogenicity indexes were classified as follows: 3, moderately pathogenic; 2, low pathogenic;1, least pathogenic; and 0, nonpathogenic.</p

Viral titers in the lungs of DBA/2J mice infected with avian H1N1 virus isolates from different pathogenicity levels.^a

a<p>Lungs were collected from mice after natural death or euthanasia upon 25% weight loss, according to our protocol.</p><p><b>Abbreviations:</b> ND, not determined; UD, undetected.</p

Transmissibility of A/shorebird/DE/300/2009 in ferrets.

<p>Viral titers were detected in (A) nasal washes and (B) rectal swabs of donor ferrets (red), direct-contact ferrets (DC, green) and respiratory-droplet–contact ferrets (RDC, blue) 14 dpi. Data from each animal are shown. Viral titers are given in terms of EID₅₀.</p

Comparison of the mean pathogenicity scores of each pathogenicity index (PI) category.

<p>Each avian H1N1 virus and the 2009 pandemic strains were assigned to a PI category based on their total pathogenicity score in DBA/2J mice. The PI-4 category includes the most pathogenic isolates; PI-3, moderately pathogenic isolates; PI-2, low pathogenic isolates; and PI-1, least pathogenic isolates. (*<i>P<0.05</i>).</p