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  • Articles  (51)
  • *Ecosystem  (50)
  • Astrophysics
  • 2005-2009  (51)
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  • 1
    Publication Date: 2008-03-04
    Description: Viruses, and more particularly phages (viruses that infect bacteria), represent one of the most abundant living entities in aquatic and terrestrial environments. The biogeography of phages has only recently been investigated and so far reveals a cosmopolitan distribution of phage genetic material (or genotypes). Here we address this cosmopolitan distribution through the analysis of phage communities in modern microbialites, the living representatives of one of the most ancient life forms on Earth. On the basis of a comparative metagenomic analysis of viral communities associated with marine (Highborne Cay, Bahamas) and freshwater (Pozas Azules II and Rio Mesquites, Mexico) microbialites, we show that some phage genotypes are geographically restricted. The high percentage of unknown sequences recovered from the three metagenomes (〉97%), the low percentage similarities with sequences from other environmental viral (n = 42) and microbial (n = 36) metagenomes, and the absence of viral genotypes shared among microbialites indicate that viruses are genetically unique in these environments. Identifiable sequences in the Highborne Cay metagenome were dominated by single-stranded DNA microphages that were not detected in any other samples examined, including sea water, fresh water, sediment, terrestrial, extreme, metazoan-associated and marine microbial mats. Finally, a marine signature was present in the phage community of the Pozas Azules II microbialites, even though this environment has not been in contact with the ocean for tens of millions of years. Taken together, these results prove that viruses in modern microbialites display biogeographical variability and suggest that they may be derived from an ancient community.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Desnues, Christelle -- Rodriguez-Brito, Beltran -- Rayhawk, Steve -- Kelley, Scott -- Tran, Tuong -- Haynes, Matthew -- Liu, Hong -- Furlan, Mike -- Wegley, Linda -- Chau, Betty -- Ruan, Yijun -- Hall, Dana -- Angly, Florent E -- Edwards, Robert A -- Li, Linlin -- Thurber, Rebecca Vega -- Reid, R Pamela -- Siefert, Janet -- Souza, Valeria -- Valentine, David L -- Swan, Brandon K -- Breitbart, Mya -- Rohwer, Forest -- England -- Nature. 2008 Mar 20;452(7185):340-3. doi: 10.1038/nature06735. Epub 2008 Mar 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, San Diego State University, San Diego, California 92182, USA. cdesnues@yahoo.fr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18311127" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriophages/classification/genetics/*isolation & purification/*physiology ; Bahamas ; *Biodiversity ; Capsid/chemistry ; Computational Biology ; DNA, Viral/analysis/genetics ; *Ecosystem ; Fresh Water/microbiology/virology ; Genome, Viral/genetics ; Genomics ; *Geography ; Geologic Sediments/microbiology/virology ; Mexico ; Molecular Sequence Data ; Phylogeny ; Proteome/metabolism ; Seawater/microbiology/virology ; *Water Microbiology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2009-09-04
    Description: Complex dynamical systems, ranging from ecosystems to financial markets and the climate, can have tipping points at which a sudden shift to a contrasting dynamical regime may occur. Although predicting such critical points before they are reached is extremely difficult, work in different scientific fields is now suggesting the existence of generic early-warning signals that may indicate for a wide class of systems if a critical threshold is approaching.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Scheffer, Marten -- Bascompte, Jordi -- Brock, William A -- Brovkin, Victor -- Carpenter, Stephen R -- Dakos, Vasilis -- Held, Hermann -- van Nes, Egbert H -- Rietkerk, Max -- Sugihara, George -- England -- Nature. 2009 Sep 3;461(7260):53-9. doi: 10.1038/nature08227.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Environmental Sciences, Wageningen University, PO Box 47, 6700 AA Wageningen, The Netherlands. marten.scheffer@wur.nl〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19727193" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Asthma/physiopathology ; Climate ; *Ecosystem ; Eutrophication ; Extinction, Biological ; Humans ; *Models, Biological ; *Models, Economic ; Seizures/physiopathology ; Stochastic Processes
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2006-05-13
    Description: By using data collected during a continuous circumnavigation of the Southern Hemisphere, we observed clear patterns in the population-genetic structure of Prochlorococcus, the most abundant photosynthetic organism on Earth, between and within the three Southern Subtropical Gyres. The same mechanisms that were previously invoked to account for the vertical distribution of ecotypes at local scales accounted for the global (horizontal) patterns we observed. Basin-scale and seasonal variations in the structure and strength of vertical stratification provide a basis for understanding large-scale horizontal distribution in genetic and physiological traits of Prochlorococcus, and perhaps of marine microbial communities in general.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bouman, Heather A -- Ulloa, Osvaldo -- Scanlan, David J -- Zwirglmaier, Katrin -- Li, William K W -- Platt, Trevor -- Stuart, Venetia -- Barlow, Ray -- Leth, Ole -- Clementson, Lesley -- Lutz, Vivian -- Fukasawa, Masao -- Watanabe, Shuichi -- Sathyendranath, Shubha -- New York, N.Y. -- Science. 2006 May 12;312(5775):918-21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratorio de Procesos Oceanograficos y Clima, Departamento de Oceanografia, and Centro de Investigacion Oceanografica en el Pacifico Sur-Oriental, Universidad de Concepcion, Casilla 160-C, Concepcion, Chile. heather@profc.udec.cl〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16690867" target="_blank"〉PubMed〈/a〉
    Keywords: Atlantic Ocean ; Biomass ; Chlorophyll/analysis ; Climate ; Colony Count, Microbial ; *Ecosystem ; Flow Cytometry ; Indian Ocean ; Light ; Oceanography ; Pacific Ocean ; Phytoplankton/*genetics/*growth & development/physiology ; Polymerase Chain Reaction ; Prochlorococcus/classification/*genetics/*growth & development/physiology ; Seasons ; Seawater/*microbiology ; Temperature ; Vinyl Compounds/analysis
    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
    Publication Date: 2006-08-26
    Description: We report atmospheric methane carbon isotope ratios (delta13CH4) from the Western Greenland ice margin spanning the Younger Dryas-to-Preboreal (YD-PB) transition. Over the recorded approximately 800 years, delta13CH4 was around -46 per mil (per thousand); that is, approximately 1 per thousand higher than in the modern atmosphere and approximately 5.5 per thousand higher than would be expected from budgets without 13C-rich anthropogenic emissions. This requires higher natural 13C-rich emissions or stronger sink fractionation than conventionally assumed. Constant delta13CH4 during the rise in methane concentration at the YD-PB transition is consistent with additional emissions from tropical wetlands, or aerobic plant CH4 production, or with a multisource scenario. A marine clathrate source is unlikely.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schaefer, Hinrich -- Whiticar, Michael J -- Brook, Edward J -- Petrenko, Vasilii V -- Ferretti, Dominic F -- Severinghaus, Jeffrey P -- New York, N.Y. -- Science. 2006 Aug 25;313(5790):1109-12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Earth and Ocean Sciences, University of Victoria, Post Office Box 3055, V8W 3P6, Canada. schaefeh@geo.oregonstate.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16931759" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Atmosphere ; Bacteria/metabolism ; Carbon Isotopes/analysis ; *Climate ; *Ecosystem ; Environment ; Greenland ; Ice/*analysis ; Methane/*analysis/metabolism ; Plants/metabolism ; 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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  • 5
    Publication Date: 2007-02-03
    Description: Since the mid-1980s, our understanding of nutrient limitation of oceanic primary production has radically changed. Mesoscale iron addition experiments (FeAXs) have unequivocally shown that iron supply limits production in one-third of the world ocean, where surface macronutrient concentrations are perennially high. The findings of these 12 FeAXs also reveal that iron supply exerts controls on the dynamics of plankton blooms, which in turn affect the biogeochemical cycles of carbon, nitrogen, silicon, and sulfur and ultimately influence the Earth climate system. However, extrapolation of the key results of FeAXs to regional and seasonal scales in some cases is limited because of differing modes of iron supply in FeAXs and in the modern and paleo-oceans. New research directions include quantification of the coupling of oceanic iron and carbon biogeochemistry.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Boyd, P W -- Jickells, T -- Law, C S -- Blain, S -- Boyle, E A -- Buesseler, K O -- Coale, K H -- Cullen, J J -- de Baar, H J W -- Follows, M -- Harvey, M -- Lancelot, C -- Levasseur, M -- Owens, N P J -- Pollard, R -- Rivkin, R B -- Sarmiento, J -- Schoemann, V -- Smetacek, V -- Takeda, S -- Tsuda, A -- Turner, S -- Watson, A J -- New York, N.Y. -- Science. 2007 Feb 2;315(5812):612-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Institute for Water and Atmospheric Research (NIWA) Centre for Chemical and Physical Oceanography, Department of Chemistry, University of Otago, Dunedin, New Zealand. pboyd@alkali.otago.ac.nz〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17272712" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Atmosphere ; Carbon/analysis/metabolism ; Carbon Dioxide ; Chlorophyll/analysis ; Climate ; Diatoms/growth & development ; *Ecosystem ; *Iron/analysis ; Oceans and Seas ; Phytoplankton/*growth & development/metabolism ; *Seawater ; Zooplankton/*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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  • 6
    Publication Date: 2009-09-19
    Description: Microorganisms have been repeatedly discovered in environments that do not support their metabolic activity. Identifying and quantifying these misplaced organisms can reveal dispersal mechanisms that shape natural microbial diversity. Using endospore germination experiments, we estimated a stable supply of thermophilic bacteria into permanently cold Arctic marine sediment at a rate exceeding 10(8) spores per square meter per year. These metabolically and phylogenetically diverse Firmicutes show no detectable activity at cold in situ temperatures but rapidly mineralize organic matter by hydrolysis, fermentation, and sulfate reduction upon induction at 50 degrees C. The closest relatives to these bacteria come from warm subsurface petroleum reservoir and ocean crust ecosystems, suggesting that seabed fluid flow from these environments is delivering thermophiles to the cold ocean. These transport pathways may broadly influence microbial community composition in the marine environment.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hubert, Casey -- Loy, Alexander -- Nickel, Maren -- Arnosti, Carol -- Baranyi, Christian -- Bruchert, Volker -- Ferdelman, Timothy -- Finster, Kai -- Christensen, Flemming Monsted -- Rosa de Rezende, Julia -- Vandieken, Verona -- Jorgensen, Bo Barker -- P 20185/Austrian Science Fund FWF/Austria -- New York, N.Y. -- Science. 2009 Sep 18;325(5947):1541-4. doi: 10.1126/science.1174012.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biogeochemistry Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany. chubert@mpi-bremen.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19762643" target="_blank"〉PubMed〈/a〉
    Keywords: Anaerobiosis ; Arctic Regions ; *Bacteria/classification/isolation & purification ; Bacterial Physiological Phenomena ; *Biodiversity ; *Cold Climate ; Cold Temperature ; *Ecosystem ; Fatty Acids, Volatile/metabolism ; Fermentation ; Geologic Sediments/*microbiology ; Hot Temperature ; Oxidation-Reduction ; Phylogeny ; Spores, Bacterial/*physiology ; Sulfates/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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  • 7
    Publication Date: 2022-05-26
    Description: Reexploring convection and its various transitions to chaotic behavior were the central themes of GFD 1981. Our principal lecturer, Dr. Edward A. Spiegel, provided both a rich historical picture and stimulating hours at the current frontiers of this topic. Before the summer was out his research lecture on "A Tale of Two Methods" elegantly merged Pierre Coullet's canonical formalism for studying dynamical systems in a central manifold and the more traditional two-timing amplitude expansions near critical points. Other lecture sequences on convection and its relation to simpler dynamical systems ranged from the fine presentations of John Guckenheimer on bifurcation theory to Fritz Busse's survey of his immense contributions to our understanding of nonlinear convection. The list of other lectures found on the following pages attests to our summer-long exposure to convection in the ocean, the atmosphere, the earth's core and mantle, and in the sun. August brought lectures on new observations of convection in the laboratories of physicists. Albert Libchaber's precise experiments on the many routes convection can take to turbulence, with parallel laboratory and numerical experiments described by J. Gollub and E. Siggia, added much to our language of inquiry.
    Description: Office of Naval Research under Contract N00014-81-G-0089.
    Keywords: Convection ; Astrophysics
    Repository Name: Woods Hole Open Access Server
    Type: Technical Report
    Format: application/pdf
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  • 8
    Publication Date: 2008-02-29
    Description: Many free-ranging predators have to make foraging decisions with little, if any, knowledge of present resource distribution and availability. The optimal search strategy they should use to maximize encounter rates with prey in heterogeneous natural environments remains a largely unresolved issue in ecology. Levy walks are specialized random walks giving rise to fractal movement trajectories that may represent an optimal solution for searching complex landscapes. However, the adaptive significance of this putative strategy in response to natural prey distributions remains untested. Here we analyse over a million movement displacements recorded from animal-attached electronic tags to show that diverse marine predators-sharks, bony fishes, sea turtles and penguins-exhibit Levy-walk-like behaviour close to a theoretical optimum. Prey density distributions also display Levy-like fractal patterns, suggesting response movements by predators to prey distributions. Simulations show that predators have higher encounter rates when adopting Levy-type foraging in natural-like prey fields compared with purely random landscapes. This is consistent with the hypothesis that observed search patterns are adapted to observed statistical patterns of the landscape. This may explain why Levy-like behaviour seems to be widespread among diverse organisms, from microbes to humans, as a 'rule' that evolved in response to patchy resource distributions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sims, David W -- Southall, Emily J -- Humphries, Nicolas E -- Hays, Graeme C -- Bradshaw, Corey J A -- Pitchford, Jonathan W -- James, Alex -- Ahmed, Mohammed Z -- Brierley, Andrew S -- Hindell, Mark A -- Morritt, David -- Musyl, Michael K -- Righton, David -- Shepard, Emily L C -- Wearmouth, Victoria J -- Wilson, Rory P -- Witt, Matthew J -- Metcalfe, Julian D -- England -- Nature. 2008 Feb 28;451(7182):1098-102. doi: 10.1038/nature06518.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK. dws@mba.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18305542" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Ecosystem ; Euphausiacea ; *Feeding Behavior ; Fractals ; Gadiformes ; *Marine Biology ; *Models, Biological ; *Motor Activity ; Oceans and Seas ; Population Density ; *Predatory Behavior ; Probability ; Seals, Earless ; Sharks ; Spheniscidae ; Tuna ; Turtles
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    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 9
    Publication Date: 2008-03-07
    Description: Complex dynamics are often shown by simple ecological models and have been clearly demonstrated in laboratory and natural systems. Yet many classes of theoretically possible dynamics are still poorly documented in nature. Here we study long-term time-series data of a midge, Tanytarsus gracilentus (Diptera: Chironomidae), in Lake Myvatn, Iceland. The midge undergoes density fluctuations of almost six orders of magnitude. Rather than regular cycles, however, these fluctuations have irregular periods of 4-7 years, indicating complex dynamics. We fit three consumer-resource models capable of qualitatively distinct dynamics to the data. Of these, the best-fitting model shows alternative dynamical states in the absence of environmental variability; depending on the initial midge densities, the model shows either fluctuations around a fixed point or high-amplitude cycles. This explains the observed complex population dynamics: high-amplitude but irregular fluctuations occur because stochastic variability causes the dynamics to switch between domains of attraction to the alternative states. In the model, the amplitude of fluctuations depends strongly on minute resource subsidies into the midge habitat. These resource subsidies may be sensitive to human-caused changes in the hydrology of the lake, with human impacts such as dredging leading to higher-amplitude fluctuations. Tanytarsus gracilentus is a key component of the Myvatn ecosystem, representing two-thirds of the secondary productivity of the lake and providing vital food resources to fish and to breeding bird populations. Therefore the high-amplitude, irregular fluctuations in midge densities generated by alternative dynamical states dominate much of the ecology of the lake.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ives, Anthony R -- Einarsson, Arni -- Jansen, Vincent A A -- Gardarsson, Arnthor -- England -- Nature. 2008 Mar 6;452(7183):84-7. doi: 10.1038/nature06610.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Zoology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA. arives@wisc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18322533" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Chironomidae/*physiology ; Computer Simulation ; *Ecosystem ; Eukaryota/physiology ; Food ; *Fresh Water ; Iceland ; Models, Biological ; Population Density ; Stochastic Processes
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    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 10
    Publication Date: 2008-03-14
    Description: Anthropogenic addition of bioavailable nitrogen to the biosphere is increasing and terrestrial ecosystems are becoming increasingly nitrogen-saturated, causing more bioavailable nitrogen to enter groundwater and surface waters. Large-scale nitrogen budgets show that an average of about 20-25 per cent of the nitrogen added to the biosphere is exported from rivers to the ocean or inland basins, indicating that substantial sinks for nitrogen must exist in the landscape. Streams and rivers may themselves be important sinks for bioavailable nitrogen owing to their hydrological connections with terrestrial systems, high rates of biological activity, and streambed sediment environments that favour microbial denitrification. Here we present data from nitrogen stable isotope tracer experiments across 72 streams and 8 regions representing several biomes. We show that total biotic uptake and denitrification of nitrate increase with stream nitrate concentration, but that the efficiency of biotic uptake and denitrification declines as concentration increases, reducing the proportion of in-stream nitrate that is removed from transport. Our data suggest that the total uptake of nitrate is related to ecosystem photosynthesis and that denitrification is related to ecosystem respiration. In addition, we use a stream network model to demonstrate that excess nitrate in streams elicits a disproportionate increase in the fraction of nitrate that is exported to receiving waters and reduces the relative role of small versus large streams as nitrate sinks.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mulholland, Patrick J -- Helton, Ashley M -- Poole, Geoffrey C -- Hall, Robert O -- Hamilton, Stephen K -- Peterson, Bruce J -- Tank, Jennifer L -- Ashkenas, Linda R -- Cooper, Lee W -- Dahm, Clifford N -- Dodds, Walter K -- Findlay, Stuart E G -- Gregory, Stanley V -- Grimm, Nancy B -- Johnson, Sherri L -- McDowell, William H -- Meyer, Judy L -- Valett, H Maurice -- Webster, Jackson R -- Arango, Clay P -- Beaulieu, Jake J -- Bernot, Melody J -- Burgin, Amy J -- Crenshaw, Chelsea L -- Johnson, Laura T -- Niederlehner, B R -- O'Brien, Jonathan M -- Potter, Jody D -- Sheibley, Richard W -- Sobota, Daniel J -- Thomas, Suzanne M -- England -- Nature. 2008 Mar 13;452(7184):202-5. doi: 10.1038/nature06686.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA. mulhollandpj@ornl.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18337819" target="_blank"〉PubMed〈/a〉
    Keywords: Agriculture ; Bacteria/metabolism ; Computer Simulation ; *Ecosystem ; Geography ; *Human Activities ; Nitrates/*analysis/*metabolism ; Nitrites/*analysis/*metabolism ; Nitrogen/analysis/metabolism ; Nitrogen Isotopes ; Plants/metabolism ; Rivers/*chemistry ; Urbanization
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    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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