Malfatti Stephanie A.

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Stephanie A.

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  • Article
    Genome of the epsilonproteobacterial chemolithoautotroph Sulfurimonas denitrificans
    (American Society for Microbiology, 2007-12-07) Sievert, Stefan M. ; Scott, Kathleen M. ; Klotz, Martin G. ; Chain, Patrick S. G. ; Hauser, Loren J. ; Hemp, James ; Hugler, Michael ; Land, Miriam L. ; Lapidus, Alla ; Larimer, Frank W. ; Lucas, Susan ; Malfatti, Stephanie A. ; Meyer, Folker ; Paulsen, Ian T. ; Ren, Qinghu ; Simon, Jörg ; USF Genomics Class
    Sulfur-oxidizing epsilonproteobacteria are common in a variety of sulfidogenic environments. These autotrophic and mixotrophic sulfur-oxidizing bacteria are believed to contribute substantially to the oxidative portion of the global sulfur cycle. In order to better understand the ecology and roles of sulfur-oxidizing epsilonproteobacteria, in particular those of the widespread genus Sulfurimonas, in biogeochemical cycles, the genome of Sulfurimonas denitrificans DSM1251 was sequenced. This genome has many features, including a larger size (2.2 Mbp), that suggest a greater degree of metabolic versatility or responsiveness to the environment than seen for most of the other sequenced epsilonproteobacteria. A branched electron transport chain is apparent, with genes encoding complexes for the oxidation of hydrogen, reduced sulfur compounds, and formate and the reduction of nitrate and oxygen. Genes are present for a complete, autotrophic reductive citric acid cycle. Many genes are present that could facilitate growth in the spatially and temporally heterogeneous sediment habitat from where Sulfurimonas denitrificans was originally isolated. Many resistance-nodulation-development family transporter genes (10 total) are present; of these, several are predicted to encode heavy metal efflux transporters. An elaborate arsenal of sensory and regulatory protein-encoding genes is in place, as are genes necessary to prevent and respond to oxidative stress.
  • Article
    The genome of deep-sea vent chemolithoautotroph Thiomicrospira crunogena XCL-2
    (Public Library of Science (PLoS), 2006-11-14) Scott, Kathleen M. ; Sievert, Stefan M. ; Abril, Fereniki N. ; Ball, Lois A. ; Barrett, Chantell J. ; Blake, Rodrigo A. ; Boller, Amanda J. ; Chain, Patrick S. G. ; Clark, Justine A. ; Davis, Carisa R. ; Detter, Chris ; Do, Kimberly F. ; Dobrinski, Kimberly P. ; Faza, Brandon I. ; Fitzpatrick, Kelly A. ; Freyermuth, Sharyn K. ; Harmer, Tara L. ; Hauser, Loren J. ; Hugler, Michael ; Kerfeld, Cheryl A. ; Klotz, Martin G. ; Kong, William W. ; Land, Miriam L. ; Lapidus, Alla ; Larimer, Frank W. ; Longo, Dana L. ; Lucas, Susan ; Malfatti, Stephanie A. ; Massey, Steven E. ; Martin, Darlene D. ; McCuddin, Zoe ; Meyer, Folker ; Moore, Jessica L. ; Ocampo, Luis H. ; Paul, John H. ; Paulsen, Ian T. ; Reep, Douglas K. ; Ren, Qinghu ; Ross, Rachel L. ; Sato, Priscila Y. ; Thomas, Phaedra ; Tinkham, Lance E. ; Zeruth, Gary T.
    Presented here is the complete genome sequence of Thiomicrospira crunogena XCL-2, representative of ubiquitous chemolithoautotrophic sulfur-oxidizing bacteria isolated from deep-sea hydrothermal vents. This gammaproteobacterium has a single chromosome (2,427,734 base pairs), and its genome illustrates many of the adaptations that have enabled it to thrive at vents globally. It has 14 methyl-accepting chemotaxis protein genes, including four that may assist in positioning it in the redoxcline. A relative abundance of coding sequences (CDSs) encoding regulatory proteins likely control the expression of genes encoding carboxysomes, multiple dissolved inorganic nitrogen and phosphate transporters, as well as a phosphonate operon, which provide this species with a variety of options for acquiring these substrates from the environment. Thiom. crunogena XCL-2 is unusual among obligate sulfur-oxidizing bacteria in relying on the Sox system for the oxidation of reduced sulfur compounds. The genome has characteristics consistent with an obligately chemolithoautotrophic lifestyle, including few transporters predicted to have organic allocrits, and Calvin-Benson-Bassham cycle CDSs scattered throughout the genome.
  • 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.