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  • *Ecosystem  (33)
  • 2000-2004  (33)
  • 1980-1984
  • 2004  (33)
  • 1
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    The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-10-02
    Description: Diatoms are unicellular algae with plastids acquired by secondary endosymbiosis. They are responsible for approximately 20% of global carbon fixation. We report the 34 million-base pair draft nuclear genome of the marine diatom Thalassiosira pseudonana and its 129 thousand-base pair plastid and 44 thousand-base pair mitochondrial genomes. Sequence and optical restriction mapping revealed 24 diploid nuclear chromosomes. We identified novel genes for silicic acid transport and formation of silica-based cell walls, high-affinity iron uptake, biosynthetic enzymes for several types of polyunsaturated fatty acids, use of a range of nitrogenous compounds, and a complete urea cycle, all attributes that allow diatoms to prosper in aquatic environments.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Armbrust, E Virginia -- Berges, John A -- Bowler, Chris -- Green, Beverley R -- Martinez, Diego -- Putnam, Nicholas H -- Zhou, Shiguo -- Allen, Andrew E -- Apt, Kirk E -- Bechner, Michael -- Brzezinski, Mark A -- Chaal, Balbir K -- Chiovitti, Anthony -- Davis, Aubrey K -- Demarest, Mark S -- Detter, J Chris -- Glavina, Tijana -- Goodstein, David -- Hadi, Masood Z -- Hellsten, Uffe -- Hildebrand, Mark -- Jenkins, Bethany D -- Jurka, Jerzy -- Kapitonov, Vladimir V -- Kroger, Nils -- Lau, Winnie W Y -- Lane, Todd W -- Larimer, Frank W -- Lippmeier, J Casey -- Lucas, Susan -- Medina, Monica -- Montsant, Anton -- Obornik, Miroslav -- Parker, Micaela Schnitzler -- Palenik, Brian -- Pazour, Gregory J -- Richardson, Paul M -- Rynearson, Tatiana A -- Saito, Mak A -- Schwartz, David C -- Thamatrakoln, Kimberlee -- Valentin, Klaus -- Vardi, Assaf -- Wilkerson, Frances P -- Rokhsar, Daniel S -- New York, N.Y. -- Science. 2004 Oct 1;306(5693):79-86.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Oceanography, University of Washington, Seattle, WA 98195, USA. armbrust@ocean.washington.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15459382" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Algal Proteins/chemistry/genetics/physiology ; Animals ; *Biological Evolution ; Cell Nucleus/genetics ; Chromosomes ; DNA/genetics ; Diatoms/chemistry/cytology/*genetics/metabolism ; *Ecosystem ; Energy Metabolism ; *Genome ; Iron/metabolism ; Light ; Light-Harvesting Protein Complexes/chemistry/genetics/metabolism ; Mitochondria/genetics ; Molecular Sequence Data ; Nitrogen/metabolism ; Photosynthesis ; Plastids/genetics ; Restriction Mapping ; Sequence Alignment ; *Sequence Analysis, DNA ; Silicic Acid/metabolism ; Symbiosis ; Urea/metabolism
    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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  • 2
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    Environmental genome shotgun sequencing of the Sargasso Sea (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-04-07
    Description: We have applied "whole-genome shotgun sequencing" to microbial populations collected en masse on tangential flow and impact filters from seawater samples collected from the Sargasso Sea near Bermuda. A total of 1.045 billion base pairs of nonredundant sequence was generated, annotated, and analyzed to elucidate the gene content, diversity, and relative abundance of the organisms within these environmental samples. These data are estimated to derive from at least 1800 genomic species based on sequence relatedness, including 148 previously unknown bacterial phylotypes. We have identified over 1.2 million previously unknown genes represented in these samples, including more than 782 new rhodopsin-like photoreceptors. Variation in species present and stoichiometry suggests substantial oceanic microbial diversity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Venter, J Craig -- Remington, Karin -- Heidelberg, John F -- Halpern, Aaron L -- Rusch, Doug -- Eisen, Jonathan A -- Wu, Dongying -- Paulsen, Ian -- Nelson, Karen E -- Nelson, William -- Fouts, Derrick E -- Levy, Samuel -- Knap, Anthony H -- Lomas, Michael W -- Nealson, Ken -- White, Owen -- Peterson, Jeremy -- Hoffman, Jeff -- Parsons, Rachel -- Baden-Tillson, Holly -- Pfannkoch, Cynthia -- Rogers, Yu-Hui -- Smith, Hamilton O -- New York, N.Y. -- Science. 2004 Apr 2;304(5667):66-74. Epub 2004 Mar 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Biological Energy Alternatives, 1901 Research Boulevard, Rockville, MD 20850, USA. jcventer@tcag.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15001713" target="_blank"〉PubMed〈/a〉
    Keywords: Archaea/*genetics ; Atlantic Ocean ; Bacteria/*genetics ; Bacteriophages/genetics ; Biodiversity ; Computational Biology ; Cyanobacteria/genetics/growth & development/metabolism ; *Ecosystem ; Eukaryotic Cells ; Genes, Archaeal ; Genes, Bacterial ; Genes, rRNA ; Genome, Archaeal ; *Genome, Bacterial ; *Genomics ; Molecular Sequence Data ; Photosynthesis ; Phylogeny ; Plasmids ; Rhodopsin/genetics ; Rhodopsins, Microbial ; Seawater/*microbiology ; *Sequence Analysis, DNA ; Water 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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  • 3
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    Distributions of microbial activities in deep subseafloor sediments (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-12-25
    Description: Diverse microbial communities and numerous energy-yielding activities occur in deeply buried sediments of the eastern Pacific Ocean. Distributions of metabolic activities often deviate from the standard model. Rates of activities, cell concentrations, and populations of cultured bacteria vary consistently from one subseafloor environment to another. Net rates of major activities principally rely on electron acceptors and electron donors from the photosynthetic surface world. At open-ocean sites, nitrate and oxygen are supplied to the deepest sedimentary communities through the underlying basaltic aquifer. In turn, these sedimentary communities may supply dissolved electron donors and nutrients to the underlying crustal biosphere.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉D'Hondt, Steven -- Jorgensen, Bo Barker -- Miller, D Jay -- Batzke, Anja -- Blake, Ruth -- Cragg, Barry A -- Cypionka, Heribert -- Dickens, Gerald R -- Ferdelman, Timothy -- Hinrichs, Kai-Uwe -- Holm, Nils G -- Mitterer, Richard -- Spivack, Arthur -- Wang, Guizhi -- Bekins, Barbara -- Engelen, Bert -- Ford, Kathryn -- Gettemy, Glen -- Rutherford, Scott D -- Sass, Henrik -- Skilbeck, C Gregory -- Aiello, Ivano W -- Guerin, Gilles -- House, Christopher H -- Inagaki, Fumio -- Meister, Patrick -- Naehr, Thomas -- Niitsuma, Sachiko -- Parkes, R John -- Schippers, Axel -- Smith, David C -- Teske, Andreas -- Wiegel, Juergen -- Padilla, Christian Naranjo -- Acosta, Juana Luz Solis -- New York, N.Y. -- Science. 2004 Dec 24;306(5705):2216-21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Ocean Drilling Program Leg 201 Shipboard Scientific Party, NASA Astrobiology Institute, University of Rhode Island Graduate School of Oceanography, South Ferry Road, Narragansett, RI 02882, USA. dhondt@gso.uri.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15618510" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteria/growth & development/isolation & purification/*metabolism ; Carbon/metabolism ; Colony Count, Microbial ; *Ecosystem ; Electron Transport ; Geologic Sediments/*microbiology ; Iron/metabolism ; Manganese/metabolism ; Methane/metabolism ; Nitrates/metabolism ; Oxidants/metabolism ; Oxidation-Reduction ; Pacific Ocean ; Peru ; Photosynthesis ; Seawater/chemistry ; Sulfates/metabolism ; Thermodynamics
    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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  • 4
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    Ecology. Salvage harvesting policies after natural disturbance (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-02-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lindenmayer, D B -- Foster, D R -- Franklin, J F -- Hunter, M L -- Noss, R F -- Schmiegelow, F A -- Perry, D -- New York, N.Y. -- Science. 2004 Feb 27;303(5662):1303.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Resource and Environmental Studies, Australian National University, Canberra, ACT, 0200, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14988539" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biodiversity ; *Disasters ; *Ecosystem ; *Fires ; *Forestry ; *Trees
    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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  • 5
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    Ecology. Ecosystem-based fishery management (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-07-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pikitch, E K -- Santora, C -- Babcock, E A -- Bakun, A -- Bonfil, R -- Conover, D O -- Dayton, P -- Doukakis, P -- Fluharty, D -- Heneman, B -- Houde, E D -- Link, J -- Livingston, P A -- Mangel, M -- McAllister, M K -- Pope, J -- Sainsbury, K J -- New York, N.Y. -- Science. 2004 Jul 16;305(5682):346-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Pew Institute for Ocean Science, Rosenstiel School of Marine and Atmospheric Science (RSMAS), University of Miami, New York, NY 10022, USA. epikitch@rsmas.miami.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15256658" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Conservation of Natural Resources ; *Ecosystem ; Environment ; *Fisheries ; *Fishes ; United States
    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
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    Ecological linkages between aboveground and belowground biota (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-06-12
    Description: All terrestrial ecosystems consist of aboveground and belowground components that interact to influence community- and ecosystem-level processes and properties. Here we show how these components are closely interlinked at the community level, reinforced by a greater degree of specificity between plants and soil organisms than has been previously supposed. As such, aboveground and belowground communities can be powerful mutual drivers, with both positive and negative feedbacks. A combined aboveground-belowground approach to community and ecosystem ecology is enhancing our understanding of the regulation and functional significance of biodiversity and of the environmental impacts of human-induced global change phenomena.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wardle, David A -- Bardgett, Richard D -- Klironomos, John N -- Setala, Heikki -- van der Putten, Wim H -- Wall, Diana H -- New York, N.Y. -- Science. 2004 Jun 11;304(5677):1629-33.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Landcare Research, Post Office Box 69, Lincoln, New Zealand. david.wardle@svek.slu.se〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15192218" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Bacterial Physiological Phenomena ; Biodiversity ; *Ecosystem ; Food Chain ; Invertebrates/*physiology ; Plant Development ; *Plant Physiological Phenomena ; *Soil/parasitology ; *Soil Microbiology ; Symbiosis
    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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  • 7
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    Large perturbations of the carbon cycle during recovery from the end-permian extinction (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-07-27
    Description: High-resolution carbon isotope measurements of multiple stratigraphic sections in south China demonstrate that the pronounced carbon isotopic excursion at the Permian-Triassic boundary was not an isolated event but the first in a series of large fluctuations that continued throughout the Early Triassic before ending abruptly early in the Middle Triassic. The unusual behavior of the carbon cycle coincides with the delayed recovery from end-Permian extinction recorded by fossils, suggesting a direct relationship between Earth system function and biological rediversification in the aftermath of Earth's most devastating mass extinction.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Payne, Jonathan L -- Lehrmann, Daniel J -- Wei, Jiayong -- Orchard, Michael J -- Schrag, Daniel P -- Knoll, Andrew H -- New York, N.Y. -- Science. 2004 Jul 23;305(5683):506-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Earth and Planetary Sciences, Harvard University, 20 Oxford Street, Cambridge, MA 02138, USA. jpayne@fas.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15273391" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biodiversity ; Calcification, Physiologic ; Carbon/*analysis/metabolism ; Carbon Isotopes/analysis ; China ; *Ecosystem ; Eukaryota ; *Fossils ; Geologic Sediments/*chemistry ; Invertebrates/anatomy & histology ; Methane/analysis ; Oxygen ; Time
    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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  • 8
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    Ecosystem properties and forest decline in contrasting long-term chronosequences (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-06-19
    Description: During succession, ecosystem development occurs; but in the long-term absence of catastrophic disturbance, a decline phase eventually follows. We studied six long-term chronosequences, in Australia, Sweden, Alaska, Hawaii, and New Zealand; for each, the decline phase was associated with a reduction in tree basal area and an increase in the substrate nitrogen-to-phosphorus ratio, indicating increasing phosphorus limitation over time. These changes were often associated with reductions in litter decomposition rates, phosphorus release from litter, and biomass and activity of decomposer microbes. Our findings suggest that the maximal biomass phase reached during succession cannot be maintained in the long-term absence of major disturbance, and that similar patterns of decline occur in forested ecosystems spanning the tropical, temperate, and boreal zones.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wardle, David A -- Walker, Lawrence R -- Bardgett, Richard D -- New York, N.Y. -- Science. 2004 Jul 23;305(5683):509-13. Epub 2004 Jun 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Forest Vegetation Ecology, Swedish University of Agricultural Sciences, SE901 83 Umea, Sweden. david.wardle@svek.slu.se〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15205475" target="_blank"〉PubMed〈/a〉
    Keywords: Alaska ; Australia ; Bacterial Physiological Phenomena ; *Biomass ; Carbon/analysis/metabolism ; Climate ; *Ecosystem ; Food Chain ; Fungi/physiology ; Geography ; Hawaii ; New Zealand ; Nitrogen/analysis/metabolism ; Phosphorus/analysis/metabolism ; Plant Development ; Soil ; Soil Microbiology ; Sweden ; Time ; *Trees/growth & development
    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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  • 9
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    Comparative losses of British butterflies, birds, and plants and the global extinction crisis (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-03-20
    Description: There is growing concern about increased population, regional, and global extinctions of species. A key question is whether extinction rates for one group of organisms are representative of other taxa. We present a comparison at the national scale of population and regional extinctions of birds, butterflies, and vascular plants from Britain in recent decades. Butterflies experienced the greatest net losses, disappearing on average from 13% of their previously occupied 10-kilometer squares. If insects elsewhere in the world are similarly sensitive, the known global extinction rates of vertebrate and plant species have an unrecorded parallel among the invertebrates, strengthening the hypothesis that the natural world is experiencing the sixth major extinction event in its history.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Thomas, J A -- Telfer, M G -- Roy, D B -- Preston, C D -- Greenwood, J J D -- Asher, J -- Fox, R -- Clarke, R T -- Lawton, J H -- New York, N.Y. -- Science. 2004 Mar 19;303(5665):1879-81.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Natural Environment Research Council (NERC) Centre for Ecology and Hydrology, Dorset Laboratory, Winfrith Technology Centre, Dorchester DT2 8ZD, UK. jat@ceh.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15031508" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biodiversity ; *Birds ; *Butterflies ; *Ecosystem ; Great Britain ; *Plants ; Population Density ; Population Dynamics
    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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  • 10
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    Lowland forest loss in protected areas of Indonesian Borneo (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-02-14
    Description: The ecology of Bornean rainforests is driven by El Nino-induced droughts that trigger synchronous fruiting among trees and bursts of faunal reproduction that sustain vertebrate populations. However, many of these species- and carbon-rich ecosystems have been destroyed by logging and conversion, which increasingly threaten protected areas. Our satellite, Geographic Information System, and field-based analyses show that from 1985 to 2001, Kalimantan's protected lowland forests declined by more than 56% (〉29,000 square kilometers). Even uninhabited frontier parks are logged to supply international markets. "Protected" forests have become increasingly isolated and deforested and their buffer zones degraded. Preserving the ecological integrity of Kalimantan's rainforests requires immediate transnational management.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Curran, L M -- Trigg, S N -- McDonald, A K -- Astiani, D -- Hardiono, Y M -- Siregar, P -- Caniago, I -- Kasischke, E -- New York, N.Y. -- Science. 2004 Feb 13;303(5660):1000-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Yale School of Forestry and Environmental Studies, 205 Prospect Street, New Haven, CT 06511, USA. lisa.curran@yale.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14963327" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biodiversity ; Borneo ; *Conservation of Natural Resources ; *Ecosystem ; Forestry ; Industry ; Population Density ; Time Factors ; *Trees/growth & development ; Tropical Climate ; Vertebrates ; Wood
    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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