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  • 1
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    Major gradients in putatively nitrifying and non-nitrifying Archaea in the deep North Atlantic (2008)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2008-11-28
    Description: Aerobic nitrification of ammonia to nitrite and nitrate is a key process in the oceanic nitrogen cycling mediated by prokaryotes. Apart from Bacteria belonging to the beta- and gamma-Proteobacteria involved in the first nitrification step, Crenarchaeota have recently been recognized as main drivers of the oxidation of ammonia to nitrite in soil as well as in the ocean, as indicated by the dominance of archaeal ammonia monooxygenase (amoA) genes over bacterial amoA. Evidence is accumulating that archaeal amoA genes are common in a wide range of marine systems. Essentially, all these reports focused on surface and mesopelagic (200-1,000 m depth) waters, where ammonia concentrations are higher than in waters below 1,000 m depth. However, Crenarchaeota are also abundant in the water column below 1,000 m, where ammonia concentrations are extremely low. Here we show that, throughout the North Atlantic Ocean, the abundance of archaeal amoA genes decreases markedly from subsurface waters to 4,000 m depth, and from subpolar to equatorial deep waters, leading to pronounced vertical and latitudinal gradients in the ratio of archaeal amoA to crenarchaeal 16S ribosomal RNA (rRNA) genes. The lack of significant copy numbers of amoA genes and the very low fixation rates of dark carbon dioxide in the bathypelagic North Atlantic suggest that most bathypelagic Crenarchaeota are not autotrophic ammonia oxidizers: most likely, they utilize organic matter and hence live heterotrophically.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Agogue, Helene -- Brink, Maaike -- Dinasquet, Julie -- Herndl, Gerhard J -- England -- Nature. 2008 Dec 11;456(7223):788-91. doi: 10.1038/nature07535. Epub 2008 Nov 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Oceanography, Royal Netherlands Institute for Sea Research (Royal NIOZ), PO Box 59, 1790 AB Den Burg, Texel, The Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19037244" target="_blank"〉PubMed〈/a〉
    Keywords: Archaea/classification/enzymology/genetics/*physiology ; Atlantic Ocean ; *Biodiversity ; Carbon Dioxide/metabolism ; Crenarchaeota/physiology ; Gene Dosage ; Genetic Variation ; Molecular Sequence Data ; Nitrogen/*metabolism ; Oxidoreductases/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 2
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    Deep carbon export from a Southern Ocean iron-fertilized diatom bloom (2012)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2012-07-20
    Description: Fertilization of the ocean by adding iron compounds has induced diatom-dominated phytoplankton blooms accompanied by considerable carbon dioxide drawdown in the ocean surface layer. However, because the fate of bloom biomass could not be adequately resolved in these experiments, the timescales of carbon sequestration from the atmosphere are uncertain. Here we report the results of a five-week experiment carried out in the closed core of a vertically coherent, mesoscale eddy of the Antarctic Circumpolar Current, during which we tracked sinking particles from the surface to the deep-sea floor. A large diatom bloom peaked in the fourth week after fertilization. This was followed by mass mortality of several diatom species that formed rapidly sinking, mucilaginous aggregates of entangled cells and chains. Taken together, multiple lines of evidence-although each with important uncertainties-lead us to conclude that at least half the bloom biomass sank far below a depth of 1,000 metres and that a substantial portion is likely to have reached the sea floor. Thus, iron-fertilized diatom blooms may sequester carbon for timescales of centuries in ocean bottom water and for longer in the sediments.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Smetacek, Victor -- Klaas, Christine -- Strass, Volker H -- Assmy, Philipp -- Montresor, Marina -- Cisewski, Boris -- Savoye, Nicolas -- Webb, Adrian -- d'Ovidio, Francesco -- Arrieta, Jesus M -- Bathmann, Ulrich -- Bellerby, Richard -- Berg, Gry Mine -- Croot, Peter -- Gonzalez, Santiago -- Henjes, Joachim -- Herndl, Gerhard J -- Hoffmann, Linn J -- Leach, Harry -- Losch, Martin -- Mills, Matthew M -- Neill, Craig -- Peeken, Ilka -- Rottgers, Rudiger -- Sachs, Oliver -- Sauter, Eberhard -- Schmidt, Maike M -- Schwarz, Jill -- Terbruggen, Anja -- Wolf-Gladrow, Dieter -- England -- Nature. 2012 Jul 18;487(7407):313-9. doi: 10.1038/nature11229.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Alfred Wegener Institute for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany. victor.smetacek@awi.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22810695" target="_blank"〉PubMed〈/a〉
    Keywords: Carbon/*metabolism ; Carbon Dioxide/metabolism ; *Carbon Sequestration ; Diatoms/metabolism/*physiology ; Iron/*metabolism ; Oceans and Seas ; Time Factors
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 3
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    Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-09-03
    Description: Recent studies suggest that unidentified prokaryotes fix inorganic carbon at globally significant rates in the immense dark ocean. Using single-cell sorting and whole-genome amplification of prokaryotes from two subtropical gyres, we obtained genomic DNA from 738 cells representing most cosmopolitan lineages. Multiple cells of Deltaproteobacteria cluster SAR324, Gammaproteobacteria clusters ARCTIC96BD-19 and Agg47, and some Oceanospirillales from the lower mesopelagic contained ribulose-1,5-bisphosphate carboxylase-oxygenase and sulfur oxidation genes. These results corroborated community DNA and RNA profiling from diverse geographic regions. The SAR324 genomes also suggested C(1) metabolism and a particle-associated life-style. Microautoradiography and fluorescence in situ hybridization confirmed bicarbonate uptake and particle association of SAR324 cells. Our study suggests potential chemolithoautotrophy in several uncultured Proteobacteria lineages that are ubiquitous in the dark oxygenated ocean and provides new perspective on carbon cycling in the ocean's largest habitat.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Swan, Brandon K -- Martinez-Garcia, Manuel -- Preston, Christina M -- Sczyrba, Alexander -- Woyke, Tanja -- Lamy, Dominique -- Reinthaler, Thomas -- Poulton, Nicole J -- Masland, E Dashiell P -- Gomez, Monica Lluesma -- Sieracki, Michael E -- DeLong, Edward F -- Herndl, Gerhard J -- Stepanauskas, Ramunas -- New York, N.Y. -- Science. 2011 Sep 2;333(6047):1296-300. doi: 10.1126/science.1203690.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Bigelow Laboratory for Ocean Sciences, 180 McKown Point Road, Post Office Box 475, West Boothbay Harbor, ME 04575, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21885783" target="_blank"〉PubMed〈/a〉
    Keywords: ATP-Binding Cassette Transporters/genetics/metabolism ; Carbon Cycle ; Carbon Dioxide/metabolism ; *Chemoautotrophic Growth ; Darkness ; Deltaproteobacteria/classification/genetics/growth & development/*metabolism ; Gammaproteobacteria/classification/genetics/growth & development/*metabolism ; Genes, Bacterial ; Genome, Bacterial ; Metagenome ; Molecular Sequence Data ; Oceans and Seas ; Oxidation-Reduction ; Phylogeny ; Ribulose-Bisphosphate Carboxylase/genetics ; Seawater/*microbiology ; Sulfur/metabolism ; Sulfur Compounds/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
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    Response to Comment on "Dilution limits dissolved organic carbon utilization in the deep ocean" (2015)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2015-12-19
    Description: Our recent finding that dilution limits dissolved organic carbon (DOC) utilization in the deep ocean has been criticized based on the common misconception that lability equates to rapid and complete utilization. Even when considering the redefinition of recalcitrant DOC recently proposed by Jiao et al., the dilution hypothesis best explains our experimental observations.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Arrieta, Jesus M -- Mayol, Eva -- Hansman, Roberta L -- Herndl, Gerhard J -- Dittmar, Thorsten -- Duarte, Carlos M -- New York, N.Y. -- Science. 2015 Dec 18;350(6267):1483. doi: 10.1126/science.aac7249. Epub 2015 Dec 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Red Sea Research Center, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia. Department of Global Change Research, Institut Mediterrani d'Estudis Avancats (IMEDEA), Consejo Superior de Investigaciones Cientificas (CSIC)/Universidad de las Islas Baleares (UIB), 07190 Esporles, Spain. jesus.arrieta@kaust.edu.sa. ; Department of Global Change Research, Institut Mediterrani d'Estudis Avancats (IMEDEA), Consejo Superior de Investigaciones Cientificas (CSIC)/Universidad de las Islas Baleares (UIB), 07190 Esporles, Spain. ; Department of Limnology and Bio-Oceanography, Division Bio-Oceanography, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria. ; Department of Limnology and Bio-Oceanography, Division Bio-Oceanography, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria. Department of Biological Oceanography, Royal Netherlands Institute for Sea Research (NIOZ), 1790AB Den Burg, Netherlands. ; Research Group for Marine Geochemistry (ICBM-MPI Bridging Group), Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Germany. ; Red Sea Research Center, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia. Department of Global Change Research, Institut Mediterrani d'Estudis Avancats (IMEDEA), Consejo Superior de Investigaciones Cientificas (CSIC)/Universidad de las Islas Baleares (UIB), 07190 Esporles, Spain.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26680189" target="_blank"〉PubMed〈/a〉
    Keywords: *Carbon Cycle ; Carbon Dioxide/*chemistry ; *Oceans and Seas ; Seawater/*chemistry/*microbiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 5
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    Ocean chemistry. Dilution limits dissolved organic carbon utilization in the deep ocean (2015)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2015-04-18
    Description: Oceanic dissolved organic carbon (DOC) is the second largest reservoir of organic carbon in the biosphere. About 72% of the global DOC inventory is stored in deep oceanic layers for years to centuries, supporting the current view that it consists of materials resistant to microbial degradation. An alternative hypothesis is that deep-water DOC consists of many different, intrinsically labile compounds at concentrations too low to compensate for the metabolic costs associated to their utilization. Here, we present experimental evidence showing that low concentrations rather than recalcitrance preclude consumption of a substantial fraction of DOC, leading to slow microbial growth in the deep ocean. These findings demonstrate an alternative mechanism for the long-term storage of labile DOC in the deep ocean, which has been hitherto largely ignored.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Arrieta, Jesus M -- Mayol, Eva -- Hansman, Roberta L -- Herndl, Gerhard J -- Dittmar, Thorsten -- Duarte, Carlos M -- New York, N.Y. -- Science. 2015 Apr 17;348(6232):331-3. doi: 10.1126/science.1258955. Epub 2015 Mar 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Global Change Research, Institut Mediterrani d'Estudis Avancats (IMEDEA), Consejo Superior de Investigaciones Cientificas (CSIC)/Universidad de las Islas Baleares (UIB), 07190 Esporles, Spain. Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia. txetxu@mail.com. ; Department of Global Change Research, Institut Mediterrani d'Estudis Avancats (IMEDEA), Consejo Superior de Investigaciones Cientificas (CSIC)/Universidad de las Islas Baleares (UIB), 07190 Esporles, Spain. ; Department of Limnology and Bio-Oceanography, Division Bio-Oceanography, University of Vienna, Althanstr. 14, 1090 Vienna, Austria. ; Department of Limnology and Bio-Oceanography, Division Bio-Oceanography, University of Vienna, Althanstr. 14, 1090 Vienna, Austria. Department of Biological Oceanography, Royal Netherlands Institute for Sea Research (NIOZ), 1790AB Den Burg, Netherlands. ; Research Group for Marine Geochemistry (ICBM-MPI Bridging Group), Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, and Max Planck Institute for Marine Microbiology (MPI), Bremen, Germany. ; Department of Global Change Research, Institut Mediterrani d'Estudis Avancats (IMEDEA), Consejo Superior de Investigaciones Cientificas (CSIC)/Universidad de las Islas Baleares (UIB), 07190 Esporles, Spain. Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia. The UWA Oceans Institute, University of Western Australia (UWA), Crawley, WA, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25883355" target="_blank"〉PubMed〈/a〉
    Keywords: Carbon/analysis ; *Carbon Cycle ; Carbon Dioxide/*chemistry ; *Oceans and Seas ; Seawater/*chemistry/*microbiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
    Electronic Resource
    Electronic Resource
    Role of bacteria in decomposition of faecal pellets egested by the epiphyte-grazing gastropod Gibbula umbilicaris (1986)
    Springer
    Marine biology 92 (1986), S. 417-424 
    Details
    ISSN: 1432-1793
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The significance of the microheterotrophic utilization of faecal pellets derived from Gibbula umbilicaris — one of the most important gastropod species in the Posidonia oceanica ecosystem around the Isle of Ischia (Italy) — was investigated by means of microcosm-experiments. Initial total organic carbon (TOC) content of faecal pellets was 32 μgC (mg faeces dry wt)-1 and declined continuously over a 2-month incubation period. The low values of TOC coincided with SEM observations of pellets which were found to consist mainly of diatom frustules and other slowly utilizable material. In a long-term experiment freshly egested faecal pellets were rapidly colonized by bacteria, which reached densities of up to 14x105 cells (mg faeces dry wt)-1 within 12 h. Thereafter bacterial numbers declined and fluctuated in a very narrow range between 2 and 3.5x105 cells (mg faeces dry wt)-1 during the two months of the investigation period. In short-term experiments (over 5 d) similar trends were observed. Peak densities of attached bacteria were followed by a decline of this population. Concurrently the number of free-living bacteria increased. This observation was confirmed by O2 consumption measurements of freshly egested faecal pellets over 24 h, where the highest O2 consumption rates were obtained after 12 h, followed by a rapid decline, thus supporting the view that detachment of bacteria may occur. Moreover, the respiration data indicate that about 4% of faecal TOC are remineralized within the first day.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00392682
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  • 7
    Electronic Resource
    Electronic Resource
    Microheterotrophic utilization of mucus released by the Mediterranean coral Cladocora cespitosa (1986)
    Springer
    Marine biology 90 (1986), S. 363-369 
    Details
    ISSN: 1432-1793
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The amount of mucus released by the Mediterranean coral Cladocora cespitosa (L.) was determined in laboratory experiments and the incorporation of mucus into bacterial biomass was investigated by means of incubation experiments in 1984. Mean mucus release was 8.5 μg (mucus dry wt) pclyp-1 h-1 and amounted to 44% of the respiratory carbon losses of the coral since mean organic carbon content of freshly collected mucus was 102.2μg C mg (mucus dry wt)-1. Due to the abundance of C. cespitosa in the shallow littoral of the Bight of Piran, the energy content of mucus released is estimated to correspond to about 20% of the phytoplankton primary production in this area. Furthermore, the carbon conversion efficiency of 20% obtained from the bacterial population during decomposition of mucus indicates the high nutritional value of C. cespitosa mucus, although bacterial carbon onto mucus particles contributes less than 0.1% to the total organic carbon pool of the mucus.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00428560
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  • 8
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    Archaeal nitrification in the ocean (2006)
    National Academy of Sciences
    Details
    Publication Date: 2006-08-07
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 9
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    Microbial diversity in the deep sea and the underexplored "rare biosphere" (2006)
    National Academy of Sciences
    Details
    Publication Date: 2006-07-31
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 10
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    Role of macroscopic particles in deep-sea oxygen consumption (2010)
    National Academy of Sciences
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    Publication Date: 2010-04-20
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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