Ocean Sampling Day Consortium, Participants (2015): Registry of samples and environmental context from the Ocean Sampling Day 2014 [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.854419
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Abstract:
The Ocean Sampling Day (OSD) is a simultaneous sampling campaign of the world's oceans which took place (for the first time) on the summer solstice (June 21st) in the year 2014. These cumulative samples, related in time, space and environmental parameters, provide insights into fundamental rules describing microbial diversity and function and contribute to the blue economy through the identification of novel, ocean-derived biotechnologies. We see OSD data as a reference data set for generations of experiments to follow in the coming decade. The present data set includes a description of each sample collected during the Ocean Sampling Day 2014 and provides contextual environmental data measured concurrently with the collection of water samples for genomic analyses.
Related to:
Kopf-Klindworth, Anna; Bicak, Mesude; Kottmann, Renzo; Schnetzer, Julia; Kostadinov, Ivaylo; Lehmann, Katja; Fernandez-Guerra, Antonio; Jeanthon, Christian; Rahav, Eyal; Ullrich, Matthias; Wichels, Antje; Gerdts, Gunnar; Paraskevi, Polymenakou; Kotoulas, Giorgos; Siam, Rania; Abdallah, Rehab Zohier; Sonnenschein, Eva C; Cariou, Thierry; O'Gara, Fergal; Jackson, Stephen; Orlic, Sandi; Steinke, Michael; Busch, Julia; Duarte, Bernardo; Cacador, Isabel; Canning-Clode, Joao; Bobrova, Oleksandra; Marteinsson, Viggo T; Reynisson, Eyjolfur; Loureiro, Isabel; Luna, Gian Marco; Quero, Grazia Marina; Löscher, Carolin R; Kremp, Anke; DeLorenzo, Marie E; Øvreås, Lise; Tolman, Jennifer; LaRoche, Julie; Penna, Antonella; Frischer, Marc; Davis, Timothy; Barker, Katherine; Meyer, Christopher P; Ramos, Sandra; Magalhães, Catarina; Jude-Lemeilleur, Florence; Aguirre-Macedo, Ma Leopoldina; Wang, Shiao; Poulton, Nicole; Jones, Michael Scott; Collin, Rachel; Fuhrman, Jed A; Conan, Pascal; Alonso, Cecilia; Stambler, Noga; Goodwin, Kelly; Yakimov, Michael M; Baltar, Federico; Bodrossy, Levente; Van De Kamp, Jodie; Frampton, Dion; Ostrowski, Martin; van Ruth, Paul; Malthouse, Paul; Claus, Simon; Deneudt, Klaas; Mortelmans, Jonas; Pitois, Sophie; Wallom, David; Salter, Ian; Costa, Rodrigo; Schroeder, Declan C; Kandil, Mahrous M; Amaral, Valentina; Biancalana, Florencia; Santana, Rafael; Pedrotti, Maria Luiza; Yoshida, Takashi; Ogata, Hiroyuki; Ingleton, Tim; Munnik, Kate; Rodríguez-Ezpeleta, Naiara; Berteaux-Lecellier, Veronique; Wecker, Patricia; Cancio, Ibon; Vaulot, Daniel; Bienhold, Christina; Ghazal, Hassan; Chaouni, Bouchra; Essayeh, Soumya; Ettamimi, Sara; Zaid, El Houcine; Boukhatem, Noureddine; Bouali, Abderrahim; Chahboune, Rajaa; Barrijal, Said; Timinouni, Mohammed; El Otmani, Fatim; Bennani, Mohamed; Mea, Marianna; Todorova, Nadezhda; Karamfilov, Ventzislav; ten Hoopen, Petra; Cochrane, Guy; L'Haridon, Stephane; Bizsel, Kemal Can; Vezzi, Alessandro; Lauro, Federico M; Martin, Patrick; Jensen, Rachelle M; Hinks, Jamie; Gebbels, Susan; Rosselli, Riccardo; De Pascale, Fabio; Schiavon, Riccardo; dos Santos, Antonina; Villar, Emilie; Pesant, Stephane; Cataletto, Bruno; Malfatti, Francesca; Edirisinghe, Ranjith; Herrera Silveira, Jorge A; Barbier, Michele; Turk, Valentina; Tinta, Tinkara; Fuller, Wayne J; Salihoglu, Ilkay; Serakinci, Nedime; Ergoren, Mahmut Cerkez; Bresnan, Eileen; Iriberri, Juan; Fronth Nyhus, Paul Anders; Bente, Edvardsen; Karlsen, Hans Erik; Golyshin, Peter N; Gasol, Josep M; Moncheva, Snejana; Dzhembekova, Nina; Johnson, Zackary; Sinigalliano, Christopher David; Gidley, Maribeth Louise; Zingone, Adriana; Danovaro, Roberto; Tsiamis, George; Clark, Melody S; Costa, Ana Cristina; El Bour, Monia; Martins, Ana; Collins, R Eric; Ducluzeau, Anne-Lise; Martinez, Jonathan; Costello, Mark J; Amaral-Zettler, Linda A; Gilbert, Jack Anthony; Davies, Neil; Field, Dawn; Glöckner, Frank Oliver (2015): The ocean sampling day consortium. GigaScience, 4(1), https://doi.org/10.1186/s13742-015-0066-5
Further details:
Kottmann, Renzo: OSD 2014 environmental data csv documentation. https://github.com/MicroB3-IS/osd-analysis/wiki/OSD-2014-environmental-data-csv-documentation
ten Hoopen, Petra; Cochrane, Guy; MicroB3 Consortium (2014): Ocean Sampling Day Handbook - Version of June 2014. Version 2.0, OSD_Handbook_v2_June_2014.pdf
ten Hoopen, Petra; Pesant, Stephane; Kottmann, Renzo; Kopf-Klindworth, Anna; Bicak, Mesude; Claus, Simon; Deneudt, Klaas; Borremans, Catherine; Thijsse, Peter; Dekeyzer, Stefanie; Schaap, Dick; Bowler, Chris; Glöckner, Frank Oliver; Cochrane, Guy (2015): Marine microbial biodiversity, bioinformatics and biotechnology (M2B3) data reporting and service standards. Standards in Genomic Sciences, 10(1), https://doi.org/10.1186/s40793-015-0001-5
Project(s):
Funding:
Seventh Framework Programme (FP7), grant/award no. 287589: MicroB3 - Microbial Biodiversity, Bioinformatics and Biotechnology
Coverage:
Median Latitude: 36.275617 * Median Longitude: -8.815968 * South-bound Latitude: -67.344000 * West-bound Longitude: -157.843510 * North-bound Latitude: 78.453333 * East-bound Longitude: 174.818567
Date/Time Start: 2014-06-12T11:20:00 * Date/Time End: 2014-07-13T07:40:00
Minimum DEPTH, water: 0 m * Maximum DEPTH, water: 80 m
Event(s):
OSD1_20140621T1110Z * Latitude Start: 50.151000 * Longitude Start: -4.130000 * Latitude End: 50.151000 * Longitude End: -4.130000 * Date/Time Start: 2014-06-21T11:10:00 * Date/Time End: 2014-06-21T11:25:00 * Campaign: OSD-Jun-2014 * Method/Device: Bottle, Niskin 10-L (NIS_10L) * Comment: [OBJECTIVE: To collect surface seawater on the summer solstice day from the L4 mooring in the Western English Channel (OSD1) and to filter the water using the standardized protocol NPL022. The filters will be sent to Germany and subsequently processed and analysed for the prokariotic fraction. The results will be part of the global campaign OSD data-set which will allow the scientific community to better understand the microbial diversity and function in the light of climate change assessment. The data-set so established will be used as a reference for future studies and the base for developing biotechnologies.][PLATFORM: Research vessel - MBA SEPIA][DEVICE REPORTED: 10 L Niskin bottle][DESCRIPTION: 20 L of surface seawater (0-2m) were aliquoted and filtered through 5 sterivex cartridge filters using a peristaltic pump.]
OSD2_20140620T1126Z * Latitude Start: 48.777800 * Longitude Start: -3.937500 * Latitude End: 48.777800 * Longitude End: -3.937500 * Date/Time Start: 2014-06-20T11:26:00 * Date/Time End: 2014-06-20T11:45:00 * Campaign: OSD-Jun-2014 * Method/Device: Bottle, Niskin 5-L (NIS_5L) * Comment: [OBJECTIVE: Our [OBJECTIVE is to contribute to the OSD dataset on marine microbial diversity and functions and possibly its analysis. We are particularly interested by the structure and fucntions of prokaryotic and eukaryotic communities and their in situ interactions.][PLATFORM: RV Neomysis][DEVICE REPORTED: 5L Niskin bottle][DESCRIPTION: clear water]
OSD3_20140620T0540Z * Latitude Start: 54.181940 * Longitude Start: 7.900000 * Latitude End: 54.181940 * Longitude End: 7.900000 * Date/Time Start: 2014-06-20T05:40:00 * Date/Time End: 2014-06-20T06:00:00 * Campaign: OSD-Jun-2014 * Method/Device: Bucket, plastic 10-L ([BUCKET-10]) * Comment: [OBJECTIVE: OSD2014 at Helgoland][PLATFORM: Aade][DEVICE REPORTED: 10L Bucket][DESCRIPTION: surface water sampling]
Parameter(s):
| # | Name | Short Name | Unit | Principal Investigator | Method/Device | Comment |
|---|---|---|---|---|---|---|
| 1 | Sample ID | Sample ID | Kottmann, Renzo | Site_Date_Depth_Protocol | ||
| 2 | Sample code/label | Sample label | Kottmann, Renzo | registered at the European Nucleotides Archive (ENA) | INSDC biosample accession number | |
| 3 | Sample code/label | Sample label | Kottmann, Renzo | registered at the European Nucleotides Archive (ENA) | INSDC bioarchive accession number | |
| 4 | Sample code/label | Sample label | Kottmann, Renzo | registered at the European Nucleotides Archive (ENA) | INSDC sample accession number(s) | |
| 5 | Accession number, genetics | Access no gen | Kottmann, Renzo | published at the European Nucleotides Archive | related to the INSDC sample accession number(s) | |
| 6 | Campaign of event | Campaign | Ocean Sampling Day Consortium, Participants | |||
| 7 | Site | Site | Kottmann, Renzo | label | ||
| 8 | Site | Site | Kottmann, Renzo | number | ||
| 9 | Event label | Event | Ocean Sampling Day Consortium, Participants | |||
| 10 | Method/Device of event | Method/Device | Ocean Sampling Day Consortium, Participants | |||
| 11 | Comment of event | Comment | Ocean Sampling Day Consortium, Participants | |||
| 12 | URI of event | URI | Ocean Sampling Day Consortium, Participants | |||
| 13 | Date/Time of event | Date/Time | Ocean Sampling Day Consortium, Participants | |||
| 14 | Latitude of event | Latitude | Ocean Sampling Day Consortium, Participants | |||
| 15 | Longitude of event | Longitude | Ocean Sampling Day Consortium, Participants | |||
| 16 | Date/Time of event 2 | Date/Time 2 | Ocean Sampling Day Consortium, Participants | |||
| 17 | Latitude of event 2 | Latitude 2 | Ocean Sampling Day Consortium, Participants | |||
| 18 | Longitude of event 2 | Longitude 2 | Ocean Sampling Day Consortium, Participants | |||
| 19 | DEPTH, water | Depth water | m | Ocean Sampling Day Consortium, Participants | Geocode | |
| 20 | Time zone | TZ | Kottmann, Renzo | of OSD site | ||
| 21 | Local Time | Local time | Kottmann, Renzo | of sampling at OSD site | ||
| 22 | Country | Country | Kottmann, Renzo | closest coast (iso3 code) | ||
| 23 | Country | Country | Kottmann, Renzo | distance between site and closest coast (metre) | ||
| 24 | Biogeographical province | BG province | Kottmann, Renzo | Longhurst (2007) registered at marineregions.org | closest to sampling site (abbreviation) | |
| 25 | Biogeographical province | BG province | Kottmann, Renzo | Longhurst (2007) registered at marineregions.org | closest to sampling site (description) | |
| 26 | Biogeographical province | BG province | Kottmann, Renzo | Longhurst (2007) registered at marineregions.org | distance between sampling site and the closest biogeographical province (decimal degrees) | |
| 27 | Large Marine ecosystem | LME | Kottmann, Renzo | closest to sampling site (description) | ||
| 28 | Large Marine ecosystem | LME | Kottmann, Renzo | distance between site and the closets LME (metre) | ||
| 29 | Geographic name/locality | Locality | Kottmann, Renzo | of OSD site | ||
| 30 | Geographic name/locality | Locality | Kottmann, Renzo | IHO General Sea Areas (1953) registered at www.marineregions.org | of ocean and sea regions | |
| 31 | Uniform resource locator/link to reference | URL ref | Kottmann, Renzo | IHO General Sea Areas (1953) registered at www.marineregions.org | of ocean and sea regions | |
| 32 | Biome | Biome | Kottmann, Renzo | full name (ENVO:ID) | ||
| 33 | Environmental feature | Env feature | Kottmann, Renzo | terms registered at EnvO, the Environmental Ontology | full name (ENVO:ID) | |
| 34 | Material | Material | Kottmann, Renzo | terms registered at EnvO, the Environmental Ontology | full name (ENVO:ID) | |
| 35 | Sample method | Sample method | Kottmann, Renzo | Protocol Label | ||
| 36 | Sample method | Sample method | Kottmann, Renzo | Quantity (Litre) | ||
| 37 | Sample method | Sample method | Kottmann, Renzo | Container | ||
| 38 | Sample method | Sample method | Kottmann, Renzo | Content | ||
| 39 | Sample method | Sample method | Kottmann, Renzo | Size-fraction, upper threshold (micrometre) | ||
| 40 | Sample method | Sample method | Kottmann, Renzo | Size-fraction, lower threshold (micrometre) | ||
| 41 | Sample method | Sample method | Kottmann, Renzo | Treatment, chemicals | ||
| 42 | Sample method | Sample method | Kottmann, Renzo | Treatment, storage | ||
| 43 | Temperature, water | Temp | °C | Kottmann, Renzo | ||
| 44 | Salinity | Sal | Kottmann, Renzo | |||
| 45 | pH | pH | Kottmann, Renzo | unknown scale | ||
| 46 | Phosphate | [PO4]3- | µmol/l | Kottmann, Renzo | ||
| 47 | Nitrate | [NO3]- | µmol/l | Kottmann, Renzo | ||
| 48 | Carbon, organic, particulate | POC | µg/l | Kottmann, Renzo | ||
| 49 | Nitrite | [NO2]- | µmol/l | Kottmann, Renzo | ||
| 50 | Carbon, organic, dissolved | DOC | µmol/l | Kottmann, Renzo | ||
| 51 | Plankton abundance | Plank | #/m3 | Kottmann, Renzo | of nano and microplankton | |
| 52 | Radiation, photosynthetically active | PAR | µmol/m2/s | Kottmann, Renzo | downward PAR | |
| 53 | Conductivity | Cond | mS/cm | Kottmann, Renzo | ||
| 54 | Primary production of carbon | PP C | mg/m3/day | Kottmann, Renzo | isotope uptake | |
| 55 | Oxygen | O2 | µmol/kg | Kottmann, Renzo | ||
| 56 | Nitrogen, organic, particulate | PON | µmol/l | Kottmann, Renzo | ||
| 57 | Plankton abundance | Plank | #/m3 | Kottmann, Renzo | of meso and macroplankton | |
| 58 | Bacteria, production as carbon | Bact prod C | mg/m3/day | Kottmann, Renzo | ||
| 59 | Nitrogen, organic, dissolved | DON | mg/l | Kottmann, Renzo | ||
| 60 | Ammonium | [NH4]+ | µmol/l | Kottmann, Renzo | ||
| 61 | Silicate | Si(OH)4 | µmol/l | Kottmann, Renzo | ||
| 62 | Turbidity (Formazin Turbidity Unit) | Turbidity | FTU | Kottmann, Renzo | ||
| 63 | Fluorometer | Fluorometer | V | Kottmann, Renzo | ||
| 64 | Chlorophyll a | Chl a | mg/m3 | Kottmann, Renzo |
License:
Creative Commons Attribution 3.0 Unported (CC-BY-3.0)
Size:
7078 data points
Download Data
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