Davis Richard E.

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Davis
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Richard E.
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  • Article
    A novel lineage of proteobacteria involved in formation of marine Fe-oxidizing microbial mat communities
    (Public Library of Science, 2007-08-01) Emerson, David ; Rentz, Jeremy A. ; Lilburn, Timothy G. ; Davis, Richard E. ; Aldrich, Henry ; Chan, Clara S. ; Moyer, Craig L.
    For decades it has been recognized that neutrophilic Fe-oxidizing bacteria (FeOB) are associated with hydrothermal venting of Fe(II)-rich fluids associated with seamounts in the world's oceans. The evidence was based almost entirely on the mineralogical remains of the microbes, which themselves had neither been brought into culture or been assigned to a specific phylogenetic clade. We have used both cultivation and cultivation-independent techniques to study Fe-rich microbial mats associated with hydrothermal venting at Loihi Seamount, a submarine volcano. Using gradient enrichment techniques, two iron-oxidizing bacteria, strains PV-1 and JV-1, were isolated. Chemolithotrophic growth was observed under microaerobic conditions; Fe(II) and Fe0 were the only energy sources that supported growth. Both strains produced filamentous stalk-like structures composed of multiple nanometer sized fibrils of Fe-oxyhydroxide. These were consistent with mineralogical structures found in the iron mats. Phylogenetic analysis of the small subunit (SSU) rRNA gene demonstrated that strains PV-1 and JV-1 were identical and formed a monophyletic group deeply rooted within the Proteobacteria. The most similar sequence (85.3% similarity) from a cultivated isolate came from Methylophaga marina. Phylogenetic analysis of the RecA and GyrB protein sequences confirmed that these strains are distantly related to other members of the Proteobacteria. A cultivation-independent analysis of the SSU rRNA gene by terminal-restriction fragment (T-RF) profiling showed that this phylotype was most common in a variety of microbial mats collected at different times and locations at Loihi. On the basis of phylogenetic and physiological data, it is proposed that isolate PV-1T ( = 1ATCC BAA-1019: JCM 14766) represents the type strain of a novel species in a new genus, Mariprofundus ferrooxydans gen. nov., sp. nov. Furthermore, the strain is the first cultured representative of a new candidatus class of the Proteobacteria that is widely distributed in deep-sea environments, Candidatus ζ (zeta)-Proteobacteria cl. nov.
  • Article
    OceanGliders: A component of the integrated GOOS
    (Frontiers Media, 2019-10-02) Testor, Pierre ; de Young, Brad ; Rudnick, Daniel L. ; Glenn, Scott ; Hayes, Daniel J. ; Lee, Craig M. ; Pattiaratchi, Charitha ; Hill, Katherine Louise ; Heslop, Emma ; Turpin, Victor ; Alenius, Pekka ; Barrera, Carlos ; Barth, John A. ; Beaird, Nicholas ; Bécu, Guislain ; Bosse, Anthony ; Bourrin, François ; Brearley, J. Alexander ; Chao, Yi ; Chen, Sue ; Chiggiato, Jacopo ; Coppola, Laurent ; Crout, Richard ; Cummings, James A. ; Curry, Beth ; Curry, Ruth G. ; Davis, Richard F. ; Desai, Kruti ; DiMarco, Steven F. ; Edwards, Catherine ; Fielding, Sophie ; Fer, Ilker ; Frajka-Williams, Eleanor ; Gildor, Hezi ; Goni, Gustavo J. ; Gutierrez, Dimitri ; Haugan, Peter M. ; Hebert, David ; Heiderich, Joleen ; Henson, Stephanie A. ; Heywood, Karen J. ; Hogan, Patrick ; Houpert, Loïc ; Huh, Sik ; Inall, Mark E. ; Ishii, Masao ; Ito, Shin-ichi ; Itoh, Sachihiko ; Jan, Sen ; Kaiser, Jan ; Karstensen, Johannes ; Kirkpatrick, Barbara ; Klymak, Jody M. ; Kohut, Josh ; Krahmann, Gerd ; Krug, Marjolaine ; McClatchie, Sam ; Marin, Frédéric ; Mauri, Elena ; Mehra, Avichal ; Meredith, Michael P. ; Meunier, Thomas ; Miles, Travis ; Morell, Julio M. ; Mortier, Laurent ; Nicholson, Sarah ; O'Callaghan, Joanne ; O'Conchubhair, Diarmuid ; Oke, Peter ; Pallás-Sanz, Enric ; Palmer, Matthew D. ; Park, Jong Jin ; Perivoliotis, Leonidas ; Poulain, Pierre Marie ; Perry, Ruth ; Queste, Bastien ; Rainville, Luc ; Rehm, Eric ; Roughan, Moninya ; Rome, Nicholas ; Ross, Tetjana ; Ruiz, Simon ; Saba, Grace ; Schaeffer, Amandine ; Schönau, Martha ; Schroeder, Katrin ; Shimizu, Yugo ; Sloyan, Bernadette M. ; Smeed, David A. ; Snowden, Derrick ; Song, Yumi ; Swart, Sebastiaan ; Tenreiro, Miguel ; Thompson, Andrew ; Tintore, Joaquin ; Todd, Robert E. ; Toro, Cesar ; Venables, Hugh J. ; Wagawa, Taku ; Waterman, Stephanie N. ; Watlington, Roy A. ; Wilson, Doug
    The OceanGliders program started in 2016 to support active coordination and enhancement of global glider activity. OceanGliders contributes to the international efforts of the Global Ocean Observation System (GOOS) for Climate, Ocean Health, and Operational Services. It brings together marine scientists and engineers operating gliders around the world: (1) to observe the long-term physical, biogeochemical, and biological ocean processes and phenomena that are relevant for societal applications; and, (2) to contribute to the GOOS through real-time and delayed mode data dissemination. The OceanGliders program is distributed across national and regional observing systems and significantly contributes to integrated, multi-scale and multi-platform sampling strategies. OceanGliders shares best practices, requirements, and scientific knowledge needed for glider operations, data collection and analysis. It also monitors global glider activity and supports the dissemination of glider data through regional and global databases, in real-time and delayed modes, facilitating data access to the wider community. OceanGliders currently supports national, regional and global initiatives to maintain and expand the capabilities and application of gliders to meet key global challenges such as improved measurement of ocean boundary currents, water transformation and storm forecast.