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Filtering by: Creator Swartzman, G. L. (Gordon L.) Remove constraint Creator: Swartzman, G. L. (Gordon L.) Advisor Giovannoni, Stephen J. Remove constraint Advisor: Giovannoni, Stephen J.

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  • A genomic and proteomic characterization of the first cultured oligotrophic marine Gammaproteobacterium from the SAR92 clade

    Creator:
    Mellbye, Brett L.
    Abstract:
    High-throughput culturing (HTC) consisting of extinction culturing in autoclaved seawater has led to the isolation and characterization of many novel strains of oligotrophic marine bacteria. Strain HTCC 2207 was isolated from the Oregon coast by the HTC method. Phylogenetic analysis based on 16S rRNA gene sequence showed that this strain...
    Resource Type:
    Honors College Thesis
    Full Text:
    THESIS OF Brett L. Mellbye for the degree of Honors Baccalaureate of Science in Microbiology presented

  • Disturbances in a marine bacterioplankton system drive community assembly towards niche-based processes

    Creator:
    Vergin, Kevin L.
    Abstract:
    Over 100 monthly bacterioplankton DNA samples, from each of the surface and 200 m depths at the Bermuda Atlantic Time-series Study (BATS) site, were analyzed for community assembly processes. Correlation networks, filtered for potential autocorrelation artifacts, were constructed for each depth. Network characteristics for the two depths were remarkably similar...
    Resource Type:
    Masters Thesis
    Full Text:
    Bacterioplankton System Drive Community Assembly Towards Niche-based Processes by Kevin L. Vergin

  • Diversity of bacterioplankton and plastid SSU rRNA genes from the eastern and western continental shelves of the United States

    Creator:
    Rappé, Michael Stephen
    Abstract:
    The phylogenetic diversity of two continental shelf picoplankton communities was examined by analyzing SSU (16S) ribosomal RNA (rRNA) genes amplified from environmental DNA with bacterial-specific primers and the polymerase chain reaction (PCR). Picoplankton populations collected from the pycnocline (10 m) over the eastern continental shelf of the United States near...
    Resource Type:
    Dissertation
    Full Text:
    years now, Terah Wright, Doug Gordon, Dr. Ena Urbach, Marcelino Suzuki, Brian Lanoil, and Dr. Katharine

  • Bacterioplankton diversity in the lower ocean mixed layer

    Creator:
    Wright, Terah Diana
    Resource Type:
    Masters Thesis
    Full Text:
    , B.C., for the Pacific Ocean physical data. I extend my appreciation to Doug Gordon, Kevin Vergin

  • Culturing uncultured environmental microorganisms

    Creator:
    Connon, Stephanie A.
    Abstract:
    Research on natural environments, over the last decade, is replete with microbial diversity studies that used culture-independent approaches. The cloning and sequencing of the 16S rRNA genes has been the driving force in the expansion of awareness about the great diversity of previously undiscovered microorganisms. Well-known uncultured groups of microorganisms...
    Resource Type:
    Dissertation
    Full Text:
    . Micro bio!. 47, pp. 49-55. Field, K. G., D. A. Gordon, T. D. Wright, M. S. Rappé, E. Urbach, K. L

  • Marine bacterioplankton abundances and distributions

    Creator:
    Morris, Robert M.
    Abstract:
    Microorganisms play key roles in ocean biogeochemistry. However, several predominant groups of uncultured bacterioplankton thought to contribute to important biogeochemical processes in the oceans are known primarily from gene cloning studies. Although these studies have greatly expanded our view of microbial diversity in the oceans, they are not quantitative and...
    Resource Type:
    Dissertation
    Full Text:
    ., Moyer, C. L. & Field, K. G. Genetic diversity in Sargasso Sea bacterioplankton. Nature 345, 60-63 (1990

  • Single-Cell Genomics of Uncultivated Marine Bacteria

    Creator:
    Landry, Zachary
    Abstract:
    Historically, the difficulty of obtaining pure cultures of abundant marine microbial plankton has an obstacle to reconstructing the underlying mechanisms of biogeochemistry in the ocean. While a number of dominant marine species from the ocean surface have been cultured, the dominant microbial plankton of the dark ocean proved far more...
    Resource Type:
    Dissertation
    Full Text:
    Sun, J., Steindler, L., Thrash, J.C., Halsey, K.H., Smith, D.P., Carter, A.E., Landry, Z.C., and

  • Proteomic analyses of marine bacteria

    Creator:
    Sowell, Sarah M.
    Abstract:
    Proteins are the metabolic machines of the cell and as such, the study of proteins could illuminate the dominant biological activities that are occurring within cells and reveal how an organism interacts with its environment. Here, we used proteomic techniques to study the abundant marine bacterium SAR11 both as an...
    Resource Type:
    Dissertation
    Full Text:
    Microbiology Initiative investigator award from the Gordon and Betty Moore Foundation. Portions of this

  • The proteomic and transcriptomic responses to iron, sulfur, and nitrogen limitation in the abundant marine bacterium Candidatus Pelagibacter ubique

    Creator:
    Smith, Daniel P.
    Abstract:
    Batch cultures of Candidatus Pelagibacter ubique were grown under iron-, organosulfur-, and nitrogen-limiting conditions to understand how this ubiquitous marine bacterium responds to and interacts with environments where growth is limited by the availability of these nutrients. Global gene expression was monitored using microarrays and quantitative mass spectrometry to observe...
    Resource Type:
    Dissertation
    Full Text:
    concentrations of unincorporated NOX - (5 nmol L-1) and NH4 + (17 nmol L-1) at the same site [29]. Therefore

  • Microbial diversity, metabolic potential, and transcriptional activity along the inner continental shelf of the Northeast Pacific Ocean

    Creator:
    Bertagnolli, Anthony D.
    Abstract:
    Continental shelves located along eastern boundary currents occupy relatively small volumes of the world’s oceans, yet are responsible for a large proportion of global primary production. The Oregon coast is among these ecosystems. Recent analyses of dissolved oxygen at shallow depths in the water column has suggested increasing episodes of...
    Resource Type:
    Dissertation
    Full Text:
    depletion of DO can occur, leading to hypoxia (DO<1.4 ml/L), severe hypoxia (DO<0.5 ml/L), and sometimes

  • Prokaryotes associated with marine crust

    Creator:
    Mason, Olivia Underwood
    Abstract:
    Oceanic crust covers nearly 70% of the Earth's surface, of which, the upper, sediment layer is estimated to harbor substantial microbial biomass. Marine crust; however, extends several kilometers beyond this surficial layer, and includes the basalt and gabbro layers. In particular, the basalt layer has high permeabilities which allows for...
    Resource Type:
    Dissertation
    Full Text:
    quantitative analyses revealed that basalts harbor 6 × 105 to 4 × 106 and 3 × 106 to 1 × 109 cells g-1 (Einen

  • Microbial Abundance and Community Analysis in Devil’s Hole, Harrington Sound, Bermuda

    Creator:
    Denman, Carmen C.
    Abstract:
    Microbial activity within elevated CO2 and oxygen depleted environments changes with density driven stratification overturn in the seasonally anoxic region of Devil’s Hole, Bermuda. The temperature gradient developed during the summer months creates a natural laboratory to study bacterial and virus population density and microbial community dynamics in the anoxic...
    Resource Type:
    Honors College Thesis
    Full Text:
    Institute of Ocean Sciences, the Gordon and Betty Moore Foundation, and the honors excellence fund

  • Microbial Abundance and Community Analysis in Devil’s Hole, Harrington Sound, Bermuda

    Creator:
    Denman, Carmen C.
    Abstract:
    Microbial activity within elevated CO2 and oxygen depleted environments changes with density driven stratification overturn in the seasonally anoxic region of Devil’s Hole, Bermuda. The temperature gradient developed during the summer months creates a natural laboratory to study bacterial and virus population density and microbial community dynamics in the anoxic...
    Resource Type:
    Honors College Thesis
    Full Text:
    Institute of Ocean Sciences, the Gordon and Betty Moore Foundation, and the honors excellence fund

  • Genomic-assisted determination of the natural nutrient requirements of the cosmopolitan marine bacterium 'Candidatus Pelagibacter ubique'

    Creator:
    Tripp, H. James
    Abstract:
    To identify factors limiting 'Candidatus Pelagibacter ubique' maximum cell density and growth rate in pure culture on seawater, the genome sequence of 'Cand. P. ubique' was analyzed, culturing experiments with organic and inorganic nutrient additions were made, and radiotracer uptake experiments were performed. The genome was sequenced, custom data mining...
    Resource Type:
    Dissertation
    Full Text:
    from Diversa Corporation and the Gordon and Betty Moore Foundation. I must also thank my wife

  • Conserved properties in the metagenome of a large bacterioplankton population

    Creator:
    Wilhelm, Larry John
    Abstract:
    Candidatus Pelagibacter ubique is the first cultured representative of the SAR11 clade, a clade that is found throughout the oceans and accounts for approximately 25% of all bacterial cells [1]. It has a streamlined genome that is the smallest of any known free-living organism. In this study the complete genome...
    Resource Type:
    Masters Thesis
    Full Text:
    Gordon and Betty Moore foundation have helped fund the larger team required to do work of this nature

  • High resolution digital imaging of bacterial cells

    Creator:
    Siebold, William A.
    Abstract:
    The most abundant clone found in ribosomal RNA clone libraries obtained from the world's oceans belongs to the SAR11 phylogenetic group of environmental marine bacteria. Imaging and counting SAR11 bacterial cells in situ has been an important research objective for the past decade. This objective has been especially challenging due...
    Resource Type:
    Masters Thesis
    Full Text:
    I. th.3 33I136 32 35f .dgSb=h..d g.....d 331311361341331321 1. 331351311371361311 ..I...r:.,o pi Ii