6e58cace-ea68-4103-8ce4-96a1afeb4835 eng utf8 dataset dataset NERC EDS UK Polar Data Centre +44 (0)1223 221400 British Antarctic Survey, High Cross, Madingley Road Cambridge Cambridgeshire CB3 0ET United Kingdom polardatacentre@bas.ac.uk https://www.bas.ac.uk/team/business-teams/information-services/uk-polar-data-centre/ information pointOfContact 2024-01-16 ISO 19115 Geographic Information - Metadata ISO 19115:2003(E) European Petroleum Survey Group (EPSG) Geodetic Parameter Registry 2008-11-12 publication European Petroleum Survey Group EPSGadministrator@iogp.org https://www.epsg-registry.org/ EPSG Geodetic Parameter Dataset The EPSG Geodetic Parameter Dataset is a structured dataset of Coordinate Reference Systems and Coordinate Transformations, accessible through this online registry. information publisher urn:ogc:def:crs:EPSG::3031 6.18.3 Bacterial and nano-flagellate enumeration and biomass calculations from samples collected in the Greenland Sea across the Fram Strait to Svalbard during May 2018 2024-01-16 creation 2024-01-16 revision 2024-01-16 publication 2024-01-16 released 1.0 https://doi.org/10.5285/6e58cace-ea68-4103-8ce4-96a1afeb4835 doi GB/NERC/BAS/PDC/01817 https://data.bas.ac.uk/ NE/P006280/1 award Please cite this item as: Mitchell, E., & Pond, D. (2024). Bacterial and nano-flagellate enumeration and biomass calculations from samples collected in the Greenland Sea across the Fram Strait to Svalbard during May 2018 (Version 1.0) [Data set]. NERC EDS UK Polar Data Centre. https://doi.org/10.5285/6e58cace-ea68-4103-8ce4-96a1afeb4835 Collection and preservation of open ocean water samples from stations along a transect up the east coastline of Greenland and then across the Fram Strait to Svalbard during May 2018. The cruise was to observe spring bloom conditions, on board the RRS James Clark Ross. A standard CTD cast was deployed to collect the samples, depths were surface, the chlorophyll maximum and a deep sample, selected to support zooplankton net sampling and other on-board experiments. Research assistants from SAMS (Scottish Association for Marine Science) were responsible for the sample collection on JR17005, Elaine Mitchell of SAMS was responsible for the sample analysis and data processing. Funding was provided from the DIAPOD - NERC thematic grant - Changing Arctic Ocean programme - NE/P006280/1. No credit. completed Mitchell, Elaine Scottish Association For Marine Science Researcher author Pond, David University of Stirling Researcher author NERC EDS UK Polar Data Centre +44 (0)1223 221400 British Antarctic Survey, High Cross, Madingley Road Cambridge Cambridgeshire CB3 0ET United Kingdom PDCServiceDesk@bas.ac.uk https://www.bas.ac.uk/team/business-teams/information-services/uk-polar-data-centre/ information pointOfContact asNeeded completed EARTH SCIENCE > Biosphere > Ecological Dynamics > Biomass EARTH SCIENCE > Biosphere > Microbiota > Biomass theme Global Change Master Directory (GCMD) Science Keywords 2026-01-27 publication 23 Global Change Data Center, Science and Exploration Directorate, Goddard Space Flight Center (GSFC) National Aeronautics and Space Administration (NASA) Greenbelt MD United States of America https://earthdata.nasa.gov/about/gcmd/global-change-master-directory-gcmd-keywords Global Change Master Directory (GCMD) Keywords The information provided on this page seeks to define how the GCMD Keywords are structured, used and accessed. It also provides information on how users can participate in the further development of the keywords. information publisher Bacteria C:N ratio Fram Strait biomass enumeration nano-flagellate theme Greenland Basin Arctic Norsk Trough Arctic Fram Strait Arctic Kongsfjord Basin Arctic place Habitats and biotopes theme GEMET - INSPIRE themes, version 1.0 2021-01-06 revision otherRestrictions no limitations to public access otherRestrictions no limitations license Open Government Licence v3.0 otherRestrictions This data is governed by the NERC Data Policy: https://www.ukri.org/who-we-are/nerc/our-policies-and-standards/nerc-data-policy/ otherRestrictions This data is governed by the NERC data policy and supplied under Open Government Licence v.3 otherRestrictions None. url url crossReference url url crossReference url url largerWorkCitation url url crossReference textTable eng utf8 biota environment oceans -5.46434 10.84316 75.3356 80.28329 2018-05-10 2018-06-08 It is recommended that careful attention be paid to the contents of any data, and that the author be contacted with any questions regarding appropriate use. If you find any errors or omissions, please report them to polardatacentre@bas.ac.uk. NERC EDS UK Polar Data Centre +44 (0)1223 221400 British Antarctic Survey, High Cross, Madingley Road Cambridge Cambridgeshire CB3 0ET United Kingdom PDCServiceDesk@bas.ac.uk https://www.bas.ac.uk/team/business-teams/information-services/uk-polar-data-centre/ information distributor text/plain text/csv bytes 46080 http://ramadda.data.bas.ac.uk/repository/entry/show?entryid=6e58cace-ea68-4103-8ce4-96a1afeb4835 WWW:LINK-1.0-http--link Get Data Download data download bytes 46080 http://ramadda.data.bas.ac.uk/repository/entry/show?entryid=6e58cace-ea68-4103-8ce4-96a1afeb4835 WWW:LINK-1.0-http--link Get Data Download data download dataset Methodology: Seawater was collected from three depths from a standard environmental CTD cast as close to net collections. Sampling depths were selected based on the PAR irradiance readings from the CTD at the surface of the water (approx. 2m) after being initially stabilised at 10m and bought back to the surface. For bacteria and nano-flagellate samples three depths were selected: surface, the Chlorophyll maximum and a deep sample at approx. 150m. 10L acid washed carboys and acid washed tubing were used to collect the water samples. The carboys were stored in either the cold room or on deck in a low light area. Location of the collected water for storage until processing was dependent on the temperature of the surface water at the point of collection. 180µl of 25% Glutaraldehyde solution, 1% (final concentration) was dispensed into 5ml cryovial tubes. 4ml of water sample was added, the vials were gently inverted and stored in a fridge at 5°C for a minimum of 4 hours (overnight if possible) for the fixative to penetrate the cells before being snap frozen in a dewer flask containing liquid nitrogen. Once frozen the samples were stored in boxes at -80°C until analysis. Laboratory analysis: Samples were removed from -80°C freezer in small batches, one or two stations at a time and allowed to defrost in the dark in a refrigerated cool box set at 4°C. Whilst waiting for the samples to defrost the SYBR green Nucleic acid I stain and Citrate buffer were prepared. Citrate buffer: dissolve 4.6g of Potassium Citrate in 50ml of de-ionised water and filter through a sterile 0.2um filter into a sterile 50ml falcon tube - use 100µl/ml. SYBR Green: Remove a micro-centrifuge tube containing a 10µl aliquot of SYBR green from the freezer and defrost. Using a pipette and sterile tip add 250µl of sterile 0.2µm filtered de-ionised water to the micro-centrifuge tube and mix. Transfer this volume to a micro-centrifuge tube fitted with a 0.2µm filter and centrifuge at 13,000rpm for 10 seconds. Remove the tube, add another 250µl of sterile 0.2µm filtered de-ionised water to the filter and re-spin as before. Remove the filter and then transfer the 510µl of SYBR green stock to a new sterile micro-centrifuge tube - use 20µl/ml. Label PE tubes with sample information, to each tube add 300µl of citrate buffer and 60µl of SYBR green stain. Add 3ml of sample to each tube, cover tube with parafilm and leave for a minimum of 30min for the stain to take. Samples were delivered to the FACSort flowcytometer sample probe using BD Discardit II 5ml sterile syringe (non-rubber) and a syringe pump that was pre-calibrated for set flow rates. Transfer stained samples to a sterile syringe, attach syringe to the FACSort machine via tubing and needles and set up the syringe in the syringe pump cradle to deliver the sample to the flow cytometer for analysis at set rates for set amounts of time. For bacteria samples were ran at 9.5µl/min for 1 minute, for Pico-plankton samples were ran at 95µl/min for 5 min, total events per second were kept to a maximum of 1000 events per second, but as close to 300-500 as possible to improve accuracy of cell counting. Sample runs were duplicated. Cell quest software was used to analyse each sample using dot plots. Three dot plots set up, FL1 vs SSC for bacteria cells with a threshold set at 20 for FL1. FL1 vs FL2 to help gate out bacteria from the remaining pico-plankton population (no counting on this plot, just for reference). FL1 vs FL3 for pico-plankton cells with a threshold set at 150 for FL1. Areas were gated on each plot for analysis, for the bacteria plot there were three gates - Total bacteria, High DNA and Low DNA. For the pico-plankton plot there were 6 gates - Total PNAN, small PNAN, Large PNAN, Total HNAN, small HNAN and large HNAN (PNAN - Photo...(18) Data collection: Standard CTD and associated software used to determine ocean parameters and define collection depths on board the ship. Sample analysis conducted on a Becton Dickinson FACSort Flow cytometer by Elaine Mitchell. Cell quest software was used to plot the events allowing categorisation of the cells into the three groups. Data from flow cytometry analysis was entered into Windows 10 Excel spreadsheets for cell enumerations, considering dilution factors and the flow rates used. Data quality: Setting up of the gates for the three sets of cell analysis was done by hand for each sample run by Elaine Mitchell. Samples for flow cytometry really should be done fresh without freezing, as freezing does cause damage to the cells which in turn can create indistinct dot plots. Gating these plots is tricky but by analysing the samples using a range of plots with different parameters and logic gates this should have reduced any errors to a minimum. asNeeded completed