http://lod.bco-dmo.org/id/dataset/3906 eng; USA utf8 dataset Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact 2013-04-05 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) Denaturing gradient gel electrophoresis (DGGE) images from eukaryotic and cyanobacterial samples from R/V Atlantic Explorer cruises at the Bermuda Atlantic Time Series Station (BATS), 2008-2010 (Plankton particle flux project) 2013-04-05 publication 2013-04-05 revision BCO-DMO Linked Data URI 2013-04-05 creation http://lod.bco-dmo.org/id/dataset/3906 Susanne Neuer Arizona State University principalInvestigator Michael W. Lomas Bermuda Institute of Ocean Sciences principalInvestigator Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. publisher Cite this dataset as: Neuer, S., Lomas, M. W. (2013) Denaturing gradient gel electrophoresis (DGGE) images from eukaryotic and cyanobacterial samples from R/V Atlantic Explorer cruises at the Bermuda Atlantic Time Series Station (BATS), 2008-2010 (Plankton particle flux project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version final) Version Date 2013-04-05 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/3906 [access date] Denaturing gradient gel electrophoresis images from eukaryotic and cyanobacterial samples. Dataset Description: &lt;p&gt;This dataset includes original denaturing gradient gel images that resulted in eukaryotic and cyanobacterial DNA sequence data obtained from the upper water column as well as from shallow drifting traps during regular BATS cruises from May 2008-April 2010.&amp;nbsp; The associated dataset contains a complete list of denaturing gradient gel results and the closest sequence matches from the NCBI database for each excised band (phylotype).&lt;/p&gt; &lt;p&gt;Associated dataset: &lt;a href=&quot;http://data.bco-dmo.org/jg/serv/BCO/BATS_phytoflux/phytoflux_BATS.html0%7Bdir=data.bco-dmo.org/jg/dir/BCO/BATS_phytoflux/,info=data.bco-dmo.org:80/jg/info/BCO/BATS_phytoflux/phytoflux_BATS%7D&quot; target=&quot;_blank&quot;&gt;phytoflux_BATS&lt;/a&gt;&lt;/p&gt; Methods and Sampling: &lt;p&gt;Sampling and Analytical Methodology:&amp;nbsp;&lt;br /&gt; Sampling was conducted monthly from May 2008-April 2010 at the Bermuda Atlantic Time-Series (BATS). Samples were collected for DNA analysis from four depths in the upper water column and from 150 m particle traps. DNA was extracted from these samples and a region of the 18S ribosomal RNA gene for eukaryotes and 16S rRNA gene for cyanobacteria was amplified by PCR using eukaryotic and cyanobacterial primers. Each amplified sample was subjected to Denaturing Gradient Gel Electrophoresis in order to “fingerprint” the community. Individual bands were excised and identified by sequence matching using the NCBI database (http://blast.ncbi.nlm.nih.gov). Quantity One software package was used to determine similarity between samples. The efficiency of recovery was determined by qPCR in order to accurately calculate the DNA present in the water column and DNA flux into particle traps. For further detail please refer to:&lt;br /&gt; Jessica Amacher, Susanne Neuer, Michael Lomas. Accepted. DNA-based molecular fingerprinting of the contribution of eukaryotic protists and cyanobacteria to particle flux at the Bermuda Atlantic Time-Series Study. Deep Sea Research part II.&lt;/p&gt; Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0752592 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0752592 completed Susanne Neuer Arizona State University 480-727-7254 College of Liberal Arts and Sciences School of Life Sciences 427 East Tyler Mall Tempe AZ 85287-4501 USA susanne.neuer@asu.edu pointOfContact Michael W. Lomas Bermuda Institute of Ocean Sciences 207-315-2567 ext 311 60 Bigelow Drive PO Box 380 East Boothbay ME 04544 United States mlomas@bigelow.org pointOfContact asNeeded Dataset Version: final Unknown image_file Sediment Trap theme None, User defined dataset_id featureType BCO-DMO Standard Parameters Sediment Trap instrument BCO-DMO Standard Instruments AE0811 AE0813 AE0816 AE0820 AE0823 AE0826 AE0829 AE0901 AE0902 AE0904 AE0907 AE0909 AE0911 AE0916 AE0919 AE0921 AE0924 AE0926 AE0928 AE1001 AE1003 AE1005 AE1006 AE1009 service Deployment Activity Bermuda AtlanticTime Series Station (BATS) Bermuda Atlantic Time Series Station (BATS) place Locations otherRestrictions otherRestrictions Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use. Ocean Carbon and Biogeochemistry http://us-ocb.org/ Ocean Carbon and Biogeochemistry The Ocean Carbon and Biogeochemistry (OCB) program focuses on the ocean's role as a component of the global Earth system, bringing together research in geochemistry, ocean physics, and ecology that inform on and advance our understanding of ocean biogeochemistry. The overall program goals are to promote, plan, and coordinate collaborative, multidisciplinary research opportunities within the U.S. research community and with international partners. Important OCB-related activities currently include: the Ocean Carbon and Climate Change (OCCC) and the North American Carbon Program (NACP); U.S. contributions to IMBER, SOLAS, CARBOOCEAN; and numerous U.S. single-investigator and medium-size research projects funded by U.S. federal agencies including NASA, NOAA, and NSF. The scientific mission of OCB is to study the evolving role of the ocean in the global carbon cycle, in the face of environmental variability and change through studies of marine biogeochemical cycles and associated ecosystems. The overarching OCB science themes include improved understanding and prediction of: 1) oceanic uptake and release of atmospheric CO2 and other greenhouse gases and 2) environmental sensitivities of biogeochemical cycles, marine ecosystems, and interactions between the two. The OCB Research Priorities (updated January 2012) include: ocean acidification; terrestrial/coastal carbon fluxes and exchanges; climate sensitivities of and change in ecosystem structure and associated impacts on biogeochemical cycles; mesopelagic ecological and biogeochemical interactions; benthic-pelagic feedbacks on biogeochemical cycles; ocean carbon uptake and storage; and expanding low-oxygen conditions in the coastal and open oceans. OCB largerWorkCitation program Composition of the plankton community and its contribution to particle flux in the Sargasso Sea https://osprey.bco-dmo.org/project/2245 Composition of the plankton community and its contribution to particle flux in the Sargasso Sea <p>The overall objective of this proposal is to investigate linkages between the presence of different key groups of phytoplankton in the euphotic zone and their contribution to particle flux at the subtropical North Atlantic time-series station BATS (Bermuda Atlantic Time-series Study) by applying a range of traditional and novel molecular techniques.</p> <p>The 'biological pump', the photosynthetically mediated transformation of dissolved inorganic carbon into particulate and dissolved organic carbon in surface ocean waters and its subsequent export to deep water, is a significant driver of the atmospheric carbon uptake by the oceans. But this "biologically pumped" production, inasmuch as it depends on the composition and activity of planktonic organisms, is susceptible to long-term climatic changes in surface ocean properties such as increased temperature and changes in nutrient supply, especially in subtropical gyres. The sub-tropical gyres and the transition zones at their boundaries play an important role in the global carbon cycle because of their vast size and generally high per area export production. As evidenced in recent studies, the biological mechanisms driving regional to basin scale variability in carbon export in these biomes is far from understood, thus limiting our ability to mechanistically explain the biological pump and to predict its possible responses in the face of environmental change. In an effort to improve this situation with an accurate assessment of the contribution of different plankton groups to overall fluxes, the investigators will test the following two specific hypotheses: 1. The long held notion that large cells and those with mineral tests are major contributors to downward particle flux needs to be re-evaluated. We hypothesize that pico and nanoplankton (also those without mineral tests) are generally important contributors to downward particle flux at BATS. Consequently, the diversity of taxonomic groups contributing to particle flux is greater than previously expected. 2. The relative contribution of taxonomic groups to downward particle flux is a function of physical forcing. We hypothesize that episodic events (e.g., winter storms and eddies) lead to a reduction in diversity of sedimenting phytoplankton (e.g., dominance by a single group such as diatoms) compared to periods marked by more stable conditions in the water column. The broader impacts include furthering knowledge of the diversity and biology of phytoplankton groups that have a significant impact on the carbon export in subtropical gyres, thereby advancing our understanding of regional to basin scale variability in the biogeochemistry of these biomes. The project provides new opportunities for undergraduate and graduate education, as well as offer research opportunities to local high school students and teachers as part of the "Ask-a-Biologist" initiative. The project also includes an international component through collaboration with a molecular ecology group in Barcelona, Spain.</p> Plankton particle flux largerWorkCitation project eng; USA oceans Bermuda AtlanticTime Series Station (BATS); Bermuda Atlantic Time Series Station (BATS) 2013-04-05 BATS site: Bermuda Atlantic Time-Series Study: 31° 45’N, 64° 10’W 0 BCO-DMO catalogue of parameters from Denaturing gradient gel electrophoresis (DGGE) images from eukaryotic and cyanobacterial samples from R/V Atlantic Explorer cruises at the Bermuda Atlantic Time Series Station (BATS), 2008-2010 (Plankton particle flux project) Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact http://lod.bco-dmo.org/id/dataset-parameter/33592.rdf Name: image_file Units: text Description: <p>Link to the pdf containing the images contained in the dataset.</p> GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact 132 https://datadocs.bco-dmo.org/file/P66Gw3EtvO5B1q/phytoflux_images.csv phytoflux_images.csv Primary data file for dataset ID 3906 download https://osprey.bco-dmo.org/dataset/3906/data/download download onLine dataset &lt;p&gt;Sampling and Analytical Methodology:&amp;nbsp;&lt;br /&gt; Sampling was conducted monthly from May 2008-April 2010 at the Bermuda Atlantic Time-Series (BATS). Samples were collected for DNA analysis from four depths in the upper water column and from 150 m particle traps. DNA was extracted from these samples and a region of the 18S ribosomal RNA gene for eukaryotes and 16S rRNA gene for cyanobacteria was amplified by PCR using eukaryotic and cyanobacterial primers. Each amplified sample was subjected to Denaturing Gradient Gel Electrophoresis in order to “fingerprint” the community. Individual bands were excised and identified by sequence matching using the NCBI database (http://blast.ncbi.nlm.nih.gov). Quantity One software package was used to determine similarity between samples. The efficiency of recovery was determined by qPCR in order to accurately calculate the DNA present in the water column and DNA flux into particle traps. For further detail please refer to:&lt;br /&gt; Jessica Amacher, Susanne Neuer, Michael Lomas. Accepted. DNA-based molecular fingerprinting of the contribution of eukaryotic protists and cyanobacteria to particle flux at the Bermuda Atlantic Time-Series Study. Deep Sea Research part II.&lt;/p&gt; Specified by the Principal Investigator(s) &lt;p&gt;Data Processing:&lt;br /&gt; Denaturing gradient gels were imaged and analyzed with the BioRad Fluor-S imager. Bands were selected and matched manually for band matrices included in these data.&lt;/p&gt; Specified by the Principal Investigator(s) asNeeded 7.x-1.1 Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact Sediment Trap Sediment Trap PI Supplied Instrument Name: Sediment Trap PI Supplied Instrument Description:Standard BATS program trap: the regular 72 hr, fixed tubes deployment as well as a 24 hr, unfixed deployment. Instrument Name: Sediment Trap Instrument Short Name:Sediment Trap Instrument Description: Sediment traps are specially designed containers deployed in the water column for periods of time to collect particles from the water column falling toward the sea floor. In general a sediment trap has a jar at the bottom to collect the sample and a broad funnel-shaped opening at the top with baffles to keep out very large objects and help prevent the funnel from clogging. This designation is used when the specific type of sediment trap was not specified by the contributing investigator. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/33/ Cruise: AE0811 AE0811 R/V Atlantic Explorer Community Standard Description International Council for the Exploration of the Sea R/V Atlantic Explorer vessel AE0811 Anthony Knap Bermuda Biological Station for Research Cruise: AE0813 AE0813 R/V Atlantic Explorer Community Standard Description International Council for the Exploration of the Sea R/V Atlantic Explorer vessel AE0813 Anthony Knap Bermuda Biological Station for Research Cruise: AE0816 AE0816 R/V Atlantic Explorer Community Standard Description International Council for the Exploration of the Sea R/V Atlantic Explorer vessel AE0816 Anthony Knap Bermuda Biological Station for Research Cruise: AE0820 AE0820 R/V Atlantic Explorer Community Standard Description International Council for the Exploration of the Sea R/V Atlantic Explorer vessel AE0820 Anthony Knap Bermuda Biological Station for Research Cruise: AE0823 AE0823 R/V Atlantic Explorer Community Standard Description International Council for the Exploration of the Sea R/V Atlantic Explorer vessel AE0823 Anthony Knap Bermuda Biological Station for Research Cruise: AE0826 AE0826 R/V Atlantic Explorer Community Standard Description International Council for the Exploration of the Sea R/V Atlantic Explorer vessel AE0826 Anthony Knap Bermuda Biological Station for Research Cruise: AE0829 AE0829 R/V Atlantic Explorer Community Standard Description International Council for the Exploration of the Sea R/V Atlantic Explorer vessel AE0829 Anthony Knap Bermuda Biological Station for Research Cruise: AE0901 AE0901 R/V Atlantic Explorer Community Standard Description International Council for the Exploration of the Sea R/V Atlantic Explorer vessel AE0901 Anthony Knap Bermuda Biological Station for Research Cruise: AE0902 AE0902 R/V Atlantic Explorer Community Standard Description International Council for the Exploration of the Sea R/V Atlantic Explorer vessel AE0902 Anthony Knap Bermuda Biological Station for Research Cruise: AE0904 AE0904 R/V Atlantic Explorer Community Standard Description International Council for the Exploration of the Sea R/V Atlantic Explorer vessel AE0904 Anthony Knap Bermuda Biological Station for Research Cruise: AE0907 AE0907 R/V Atlantic Explorer Community Standard Description International Council for the Exploration of the Sea R/V Atlantic Explorer vessel AE0907 Anthony Knap Bermuda Biological Station for Research Cruise: AE0909 AE0909 R/V Atlantic Explorer Community Standard Description International Council for the Exploration of the Sea R/V Atlantic Explorer vessel AE0909 Anthony Knap Bermuda Biological Station for Research Cruise: AE0911 AE0911 R/V Atlantic Explorer Community Standard Description International Council for the Exploration of the Sea R/V Atlantic Explorer vessel AE0911 Anthony Knap Bermuda Biological Station for Research Cruise: AE0916 AE0916 R/V Atlantic Explorer Community Standard Description International Council for the Exploration of the Sea R/V Atlantic Explorer vessel AE0916 Anthony Knap Bermuda Biological Station for Research Cruise: AE0919 AE0919 R/V Atlantic Explorer Community Standard Description International Council for the Exploration of the Sea R/V Atlantic Explorer vessel AE0919 Anthony Knap Bermuda Biological Station for Research Cruise: AE0921 AE0921 R/V Atlantic Explorer Community Standard Description International Council for the Exploration of the Sea R/V Atlantic Explorer vessel AE0921 Anthony Knap Bermuda Biological Station for Research Cruise: AE0924 AE0924 R/V Atlantic Explorer Community Standard Description International Council for the Exploration of the Sea R/V Atlantic Explorer vessel AE0924 Anthony Knap Bermuda Biological Station for Research Cruise: AE0926 AE0926 R/V Atlantic Explorer Community Standard Description International Council for the Exploration of the Sea R/V Atlantic Explorer vessel AE0926 Anthony Knap Bermuda Biological Station for Research Cruise: AE0928 AE0928 R/V Atlantic Explorer Community Standard Description International Council for the Exploration of the Sea R/V Atlantic Explorer vessel AE0928 Anthony Knap Bermuda Biological Station for Research Cruise: AE1001 AE1001 R/V Atlantic Explorer Community Standard Description International Council for the Exploration of the Sea R/V Atlantic Explorer vessel AE1001 Anthony Knap Bermuda Biological Station for Research Cruise: AE1003 AE1003 R/V Atlantic Explorer Community Standard Description International Council for the Exploration of the Sea R/V Atlantic Explorer vessel AE1003 Anthony Knap Bermuda Biological Station for Research Cruise: AE1005 AE1005 R/V Atlantic Explorer Community Standard Description International Council for the Exploration of the Sea R/V Atlantic Explorer vessel AE1005 Anthony Knap Bermuda Biological Station for Research Cruise: AE1006 AE1006 R/V Atlantic Explorer Community Standard Description International Council for the Exploration of the Sea R/V Atlantic Explorer vessel AE1006 Lilia Jackman Bermuda Biological Station for Research Cruise: AE1009 AE1009 R/V Atlantic Explorer Community Standard Description International Council for the Exploration of the Sea R/V Atlantic Explorer vessel AE1009 Anthony Knap Bermuda Biological Station for Research R/V Atlantic Explorer Community Standard Description International Council for the Exploration of the Sea R/V Atlantic Explorer vessel