Sczyrba Alexander

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Sczyrba
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Alexander
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  • Article
    Genomic and metabolic diversity of Marine Group I Thaumarchaeota in the mesopelagic of two subtropical gyres
    (Public Library of Science, 2014-04-17) Swan, Brandon K. ; Chaffin, Mark D. ; Martinez-Garcia, Manuel ; Morrison, Hilary G. ; Field, Erin K. ; Poulton, Nicole J. ; Masland, E. Dashiell P. ; Harris, Christopher C. ; Sczyrba, Alexander ; Chain, Patrick S. G. ; Koren, Sergey ; Woyke, Tanja ; Stepanauskas, Ramunas
    Marine Group I (MGI) Thaumarchaeota are one of the most abundant and cosmopolitan chemoautotrophs within the global dark ocean. To date, no representatives of this archaeal group retrieved from the dark ocean have been successfully cultured. We used single cell genomics to investigate the genomic and metabolic diversity of thaumarchaea within the mesopelagic of the subtropical North Pacific and South Atlantic Ocean. Phylogenetic and metagenomic recruitment analysis revealed that MGI single amplified genomes (SAGs) are genetically and biogeographically distinct from existing thaumarchaea cultures obtained from surface waters. Confirming prior studies, we found genes encoding proteins for aerobic ammonia oxidation and the hydrolysis of urea, which may be used for energy production, as well as genes involved in 3-hydroxypropionate/4-hydroxybutyrate and oxidative tricarboxylic acid pathways. A large proportion of protein sequences identified in MGI SAGs were absent in the marine cultures Cenarchaeum symbiosum and Nitrosopumilus maritimus, thus expanding the predicted protein space for this archaeal group. Identifiable genes located on genomic islands with low metagenome recruitment capacity were enriched in cellular defense functions, likely in response to viral infections or grazing. We show that MGI Thaumarchaeota in the dark ocean may have more flexibility in potential energy sources and adaptations to biotic interactions than the existing, surface-ocean cultures.
  • Article
    Insights into the phylogeny and coding potential of microbial dark matter
    (Nature Publishing Group, 2013-07-14) Rinke, Christian ; Schwientek, Patrick ; Sczyrba, Alexander ; Ivanova, Natalia N. ; Anderson, Iain J. ; Cheng, Jan-Fang ; Darling, Aaron ; Malfatti, Stephanie A. ; Swan, Brandon K. ; Gies, Esther A. ; Dodsworth, Jeremy A. ; Hedlund, Brian P. ; Tsiamis, Georgios ; Sievert, Stefan M. ; Liu, Wen-Tso ; Eisen, Jonathan A. ; Hallam, Steven J. ; Kyrpides, Nikos C. ; Stepanauskas, Ramunas ; Rubin, Edward M. ; Hugenholtz, Philip ; Woyke, Tanja
    Genome sequencing enhances our understanding of the biological world by providing blueprints for the evolutionary and functional diversity that shapes the biosphere. However, microbial genomes that are currently available are of limited phylogenetic breadth, owing to our historical inability to cultivate most microorganisms in the laboratory. We apply single-cell genomics to target and sequence 201 uncultivated archaeal and bacterial cells from nine diverse habitats belonging to 29 major mostly uncharted branches of the tree of life, so-called ‘microbial dark matter’. With this additional genomic information, we are able to resolve many intra- and inter-phylum-level relationships and to propose two new superphyla. We uncover unexpected metabolic features that extend our understanding of biology and challenge established boundaries between the three domains of life. These include a novel amino acid use for the opal stop codon, an archaeal-type purine synthesis in Bacteria and complete sigma factors in Archaea similar to those in Bacteria. The single-cell genomes also served to phylogenetically anchor up to 20% of metagenomic reads in some habitats, facilitating organism-level interpretation of ecosystem function. This study greatly expands the genomic representation of the tree of life and provides a systematic step towards a better understanding of biological evolution on our planet.