Flow cytometry dataset from CTD casts showing the abundance of microorganisms (smaller than 20 µm) during the Arctic MOSAiC expedition
This dataset gives an overview of the abundance of microorganisms (smaller than 20 µm) enumerated using flow cytometry (FCM) during the Multidisciplinary drifting observatory for the study of Arctic Climate (MOSAiC) sampled from ship-based and on-ice CTD rosettes during leg 1, 2, 3, 4 and 5 (Novembe...
Main Authors: | , , , , , , , , , , , , , , , , , , , |
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Format: | Dataset |
Language: | English |
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PANGAEA
2023
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Online Access: | https://doi.pangaea.de/10.1594/PANGAEA.963430 https://doi.org/10.1594/PANGAEA.963430 |
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ftpangaea:oai:pangaea.de:doi:10.1594/PANGAEA.963430 |
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record_format |
openpolar |
institution |
Open Polar |
collection |
PANGAEA - Data Publisher for Earth & Environmental Science |
op_collection_id |
ftpangaea |
language |
English |
topic |
Acoustic focusing cytometer Thermo Fisher Attune NxT [20 mW 488 nm (blue) laser] Activity description Arctic Arctic Ocean Cast number Collector CTD/Rosette CTD-RO DATE/TIME Depth bathymetric water Device type Event label Feature flow cytometry Flow cytometry system Becton Dickinson FACSCalibur HAVOC Heterotrophic nanophytoplankton Heterotrophic prokaryotes large medium very large Heterotrophic prokaryotes with relatively high nucleic acid Heterotrophic prokaryotes with relatively low nucleic acid LATITUDE Leg Number LONGITUDE microbial abundance MOSAiC MOSAiC_ECO MOSAiC20192020 MOSAiC expedition Multidisciplinary drifting Observatory for the Study of Arctic Climate Orange and red fluorescing nanophytoplankton Orange and red fluorescing picophytoplankton Orange fluorescing prokaryote picophytoplankton Polarstern PS122/1 PS122/1_10-44 PS122/1_7-49 PS122/1_8-46 |
spellingShingle |
Acoustic focusing cytometer Thermo Fisher Attune NxT [20 mW 488 nm (blue) laser] Activity description Arctic Arctic Ocean Cast number Collector CTD/Rosette CTD-RO DATE/TIME Depth bathymetric water Device type Event label Feature flow cytometry Flow cytometry system Becton Dickinson FACSCalibur HAVOC Heterotrophic nanophytoplankton Heterotrophic prokaryotes large medium very large Heterotrophic prokaryotes with relatively high nucleic acid Heterotrophic prokaryotes with relatively low nucleic acid LATITUDE Leg Number LONGITUDE microbial abundance MOSAiC MOSAiC_ECO MOSAiC20192020 MOSAiC expedition Multidisciplinary drifting Observatory for the Study of Arctic Climate Orange and red fluorescing nanophytoplankton Orange and red fluorescing picophytoplankton Orange fluorescing prokaryote picophytoplankton Polarstern PS122/1 PS122/1_10-44 PS122/1_7-49 PS122/1_8-46 Müller, Oliver Fong, Allison A Snoeijs-Leijonmalm, Pauline Creamean, Jessie Olsen, Lasse Mørk Eggers, Lena Grosse, Julia Hoppe, Clara Jule Marie Torstensson, Anders Heitman, Laura Balmonte, John Paul Chamberlain, Emelia Dietrich, Ulrike Larsen, Aud Petelenz, Elzbieta Tsagaraki, Tatiana M Mayers, Kyle Langvad, Maria Granskog, Mats A Bratbak, Gunnar Flow cytometry dataset from CTD casts showing the abundance of microorganisms (smaller than 20 µm) during the Arctic MOSAiC expedition |
topic_facet |
Acoustic focusing cytometer Thermo Fisher Attune NxT [20 mW 488 nm (blue) laser] Activity description Arctic Arctic Ocean Cast number Collector CTD/Rosette CTD-RO DATE/TIME Depth bathymetric water Device type Event label Feature flow cytometry Flow cytometry system Becton Dickinson FACSCalibur HAVOC Heterotrophic nanophytoplankton Heterotrophic prokaryotes large medium very large Heterotrophic prokaryotes with relatively high nucleic acid Heterotrophic prokaryotes with relatively low nucleic acid LATITUDE Leg Number LONGITUDE microbial abundance MOSAiC MOSAiC_ECO MOSAiC20192020 MOSAiC expedition Multidisciplinary drifting Observatory for the Study of Arctic Climate Orange and red fluorescing nanophytoplankton Orange and red fluorescing picophytoplankton Orange fluorescing prokaryote picophytoplankton Polarstern PS122/1 PS122/1_10-44 PS122/1_7-49 PS122/1_8-46 |
description |
This dataset gives an overview of the abundance of microorganisms (smaller than 20 µm) enumerated using flow cytometry (FCM) during the Multidisciplinary drifting observatory for the study of Arctic Climate (MOSAiC) sampled from ship-based and on-ice CTD rosettes during leg 1, 2, 3, 4 and 5 (November 2019 – September 2020). Additional expedition and sampling details can be found in the ECO-overview paper (Fong et al., to be submitted to Elementa). We thank all persons involved in the expedition of the Research Vessel Polarstern during MOSAiC in 2019-2020 (AWI_PS122_00) as listed in Nixdorf et al. (2021). Flow cytometry (FCM) is a fast, high-throughput method to enumerate the abundance of microorganism (smaller than 20 µm). FCM uses the hydrodynamic focusing of a laminar flow to separate and line up microscopic particles. When particles pass a laser beam, the generated light scattering can be used to estimate their cell size, obtain information about cell granularity and surface characteristics and determine fluorescence from inherent pigments or applied stains, such as DNA binding ones. Photosynthetic microorganisms have auto-fluorescent pigments, such as chlorophylls which in combination with the light scattering properties (cell size) or surface properties, can be used to group them into clusters of similar or identical organism types. Heterotrophic microorganisms, including archaea, bacteria and heterotrophic nanoflagellates, and virus do not have fluorescent pigments and require staining, for example using SYBR Green to stain Nucleic Acids (DNA/RNA) in order to distinguish these cells from other organic and inorganic particles in the sample. Samples for flow cytometric analysis were taken in triplicates or quadruplicates of 1.8 mL of sample water and fixed with 36 μL 25 % glutaraldehyde (0.5 % final concentration) at 4 °C in the dark for approximately 2 hours, then flash frozen in liquid nitrogen and stored at -80 °C until analysis. The abundance of pico- and nano-sized phytoplankton and heterotrophic ... |
format |
Dataset |
author |
Müller, Oliver Fong, Allison A Snoeijs-Leijonmalm, Pauline Creamean, Jessie Olsen, Lasse Mørk Eggers, Lena Grosse, Julia Hoppe, Clara Jule Marie Torstensson, Anders Heitman, Laura Balmonte, John Paul Chamberlain, Emelia Dietrich, Ulrike Larsen, Aud Petelenz, Elzbieta Tsagaraki, Tatiana M Mayers, Kyle Langvad, Maria Granskog, Mats A Bratbak, Gunnar |
author_facet |
Müller, Oliver Fong, Allison A Snoeijs-Leijonmalm, Pauline Creamean, Jessie Olsen, Lasse Mørk Eggers, Lena Grosse, Julia Hoppe, Clara Jule Marie Torstensson, Anders Heitman, Laura Balmonte, John Paul Chamberlain, Emelia Dietrich, Ulrike Larsen, Aud Petelenz, Elzbieta Tsagaraki, Tatiana M Mayers, Kyle Langvad, Maria Granskog, Mats A Bratbak, Gunnar |
author_sort |
Müller, Oliver |
title |
Flow cytometry dataset from CTD casts showing the abundance of microorganisms (smaller than 20 µm) during the Arctic MOSAiC expedition |
title_short |
Flow cytometry dataset from CTD casts showing the abundance of microorganisms (smaller than 20 µm) during the Arctic MOSAiC expedition |
title_full |
Flow cytometry dataset from CTD casts showing the abundance of microorganisms (smaller than 20 µm) during the Arctic MOSAiC expedition |
title_fullStr |
Flow cytometry dataset from CTD casts showing the abundance of microorganisms (smaller than 20 µm) during the Arctic MOSAiC expedition |
title_full_unstemmed |
Flow cytometry dataset from CTD casts showing the abundance of microorganisms (smaller than 20 µm) during the Arctic MOSAiC expedition |
title_sort |
flow cytometry dataset from ctd casts showing the abundance of microorganisms (smaller than 20 µm) during the arctic mosaic expedition |
publisher |
PANGAEA |
publishDate |
2023 |
url |
https://doi.pangaea.de/10.1594/PANGAEA.963430 https://doi.org/10.1594/PANGAEA.963430 |
op_coverage |
MEDIAN LATITUDE: 85.263782 * MEDIAN LONGITUDE: 53.008084 * SOUTH-BOUND LATITUDE: 79.205856 * WEST-BOUND LONGITUDE: -35.676758 * NORTH-BOUND LATITUDE: 89.072990 * EAST-BOUND LONGITUDE: 121.007309 * DATE/TIME START: 2019-11-14T03:20:00 * DATE/TIME END: 2020-09-25T08:59:00 * MINIMUM DEPTH, water: 1 m * MAXIMUM DEPTH, water: 4458 m |
long_lat |
ENVELOPE(-35.676758,121.007309,89.072990,79.205856) |
geographic |
Arctic Arctic Ocean |
geographic_facet |
Arctic Arctic Ocean |
genre |
Arctic Arctic Ocean Phytoplankton |
genre_facet |
Arctic Arctic Ocean Phytoplankton |
op_relation |
Larsen, L B; Larsen, Aud; Thyrhaug, Runar; Bratbak, Gunnar; Sandaa, Ruth-Anne (2008): Response of marine viral populations to a nutrient induced phytoplankton bloom at different pCO2 levels. Biogeosciences, 5(2), 523-533, https://doi.org/10.5194/bg-5-523-2008 Marie, Dominique; Brussaard, Corina P D; Thyrhaug, Runar; Bratbak, Gunnar; Vaulot, Daniel (1999): Enumeration of Marine Viruses in Culture and Natural. Applied and Environmental Microbiology, 65(1), 45-52, https://doi.org/10.1128/AEM.65.1.45-52.1999 Neeley, Aimee; Soto, Inia; Proctor, Christopher W (2023): Standards and Best Practices For Reporting Flow Cytometry Observations: a technical manual. Version 1.1. UNESCO/IOC, https://doi.org/10.25607/OBP-1864.2 Nixdorf, Uwe; Dethloff, Klaus; Rex, Markus; Shupe, Matthew D; Sommerfeld, Anja; Perovich, Donald K; Nicolaus, Marcel; Heuzé, Céline; Rabe, Benjamin; Loose, Brice; Damm, Ellen; Gradinger, Rolf; Fong, Allison A; Maslowski, Wieslaw; Rinke, Annette; Kwok, Ronald; Spreen, Gunnar; Wendisch, Manfred; Herber, Andreas; Hirsekorn, Marius; Mohaupt, Verena; Frickenhaus, Stephan; Immerz, Antonia; Weiss-Tuider, Katharina; König, Bjela; Mengedoht, Dirk; Regnery, Julia; Gerchow, Peter; Ransby, Daniela; Krumpen, Thomas; Morgenstern, Anne; Haas, Christian; Kanzow, Torsten; Rack, Frank R; Saitzev, Vladimir; Sokolov, Vladimir; Makarov, Alexander; Schwarze, Stefan; Wunderlich, Thomas; Wurr, Karsten; Boetius, Antje (2021): MOSAiC Extended Acknowledgement. Zenodo, https://doi.org/10.5281/zenodo.5179738 Thyssen, Melilotus; Grégori, Gérald; Créach, Véronique; Lahbib, Soumaya; Dugenne, Mathilde; Aardema, Hedy M; Artigas, Luis Felipe; Huang, Bangqin; Barani, Aude; Beaugeard, Laureen; Bellaaj-Zouari, Amel; Beran, Alfred; Casotti, Raffaella; Del Amo, Yolanda; Denis, Michel; Dubelaar, George BJ; Endres, Sonja; Haraguchi, Lumi; Karlson, Bengt; Lambert, Christophe; Louchart, Arnaud; Marie, Dominique; Moncoiffé, Gwenaëlle; Pecqueur, David; Ribalet, François; Rijkeboer, Machteld; Silovic, Tina; Silva, Ricardo; Marro, Sophie; Sosik, Heidi M; Sourisseau, Marc; Tarran, Glen A; Van Oostende, Nicolas; Zhao, Li; Zheng, Shan (2022): Interoperable vocabulary for marine microbial flow cytometry. Frontiers in Marine Science, 9, 975877, https://doi.org/10.3389/fmars.2022.975877 Zubkov, M V; Burkill, P H; Topping, J N (2006): Flow cytometric enumeration of DNA-stained oceanic planktonic protists. Journal of Plankton Research, 29(1), 79-86, https://doi.org/10.1093/plankt/fbl059 https://doi.pangaea.de/10.1594/PANGAEA.963430 https://doi.org/10.1594/PANGAEA.963430 |
op_rights |
CC-BY-4.0: Creative Commons Attribution 4.0 International Access constraints: unrestricted info:eu-repo/semantics/openAccess |
op_doi |
https://doi.org/10.1594/PANGAEA.96343010.5194/bg-5-523-200810.1128/AEM.65.1.45-52.199910.25607/OBP-1864.210.5281/zenodo.517973810.3389/fmars.2022.97587710.1093/plankt/fbl059 |
_version_ |
1811635323616100352 |
spelling |
ftpangaea:oai:pangaea.de:doi:10.1594/PANGAEA.963430 2024-09-30T14:30:19+00:00 Flow cytometry dataset from CTD casts showing the abundance of microorganisms (smaller than 20 µm) during the Arctic MOSAiC expedition Müller, Oliver Fong, Allison A Snoeijs-Leijonmalm, Pauline Creamean, Jessie Olsen, Lasse Mørk Eggers, Lena Grosse, Julia Hoppe, Clara Jule Marie Torstensson, Anders Heitman, Laura Balmonte, John Paul Chamberlain, Emelia Dietrich, Ulrike Larsen, Aud Petelenz, Elzbieta Tsagaraki, Tatiana M Mayers, Kyle Langvad, Maria Granskog, Mats A Bratbak, Gunnar MEDIAN LATITUDE: 85.263782 * MEDIAN LONGITUDE: 53.008084 * SOUTH-BOUND LATITUDE: 79.205856 * WEST-BOUND LONGITUDE: -35.676758 * NORTH-BOUND LATITUDE: 89.072990 * EAST-BOUND LONGITUDE: 121.007309 * DATE/TIME START: 2019-11-14T03:20:00 * DATE/TIME END: 2020-09-25T08:59:00 * MINIMUM DEPTH, water: 1 m * MAXIMUM DEPTH, water: 4458 m 2023 text/tab-separated-values, 13768 data points https://doi.pangaea.de/10.1594/PANGAEA.963430 https://doi.org/10.1594/PANGAEA.963430 en eng PANGAEA Larsen, L B; Larsen, Aud; Thyrhaug, Runar; Bratbak, Gunnar; Sandaa, Ruth-Anne (2008): Response of marine viral populations to a nutrient induced phytoplankton bloom at different pCO2 levels. Biogeosciences, 5(2), 523-533, https://doi.org/10.5194/bg-5-523-2008 Marie, Dominique; Brussaard, Corina P D; Thyrhaug, Runar; Bratbak, Gunnar; Vaulot, Daniel (1999): Enumeration of Marine Viruses in Culture and Natural. Applied and Environmental Microbiology, 65(1), 45-52, https://doi.org/10.1128/AEM.65.1.45-52.1999 Neeley, Aimee; Soto, Inia; Proctor, Christopher W (2023): Standards and Best Practices For Reporting Flow Cytometry Observations: a technical manual. Version 1.1. UNESCO/IOC, https://doi.org/10.25607/OBP-1864.2 Nixdorf, Uwe; Dethloff, Klaus; Rex, Markus; Shupe, Matthew D; Sommerfeld, Anja; Perovich, Donald K; Nicolaus, Marcel; Heuzé, Céline; Rabe, Benjamin; Loose, Brice; Damm, Ellen; Gradinger, Rolf; Fong, Allison A; Maslowski, Wieslaw; Rinke, Annette; Kwok, Ronald; Spreen, Gunnar; Wendisch, Manfred; Herber, Andreas; Hirsekorn, Marius; Mohaupt, Verena; Frickenhaus, Stephan; Immerz, Antonia; Weiss-Tuider, Katharina; König, Bjela; Mengedoht, Dirk; Regnery, Julia; Gerchow, Peter; Ransby, Daniela; Krumpen, Thomas; Morgenstern, Anne; Haas, Christian; Kanzow, Torsten; Rack, Frank R; Saitzev, Vladimir; Sokolov, Vladimir; Makarov, Alexander; Schwarze, Stefan; Wunderlich, Thomas; Wurr, Karsten; Boetius, Antje (2021): MOSAiC Extended Acknowledgement. Zenodo, https://doi.org/10.5281/zenodo.5179738 Thyssen, Melilotus; Grégori, Gérald; Créach, Véronique; Lahbib, Soumaya; Dugenne, Mathilde; Aardema, Hedy M; Artigas, Luis Felipe; Huang, Bangqin; Barani, Aude; Beaugeard, Laureen; Bellaaj-Zouari, Amel; Beran, Alfred; Casotti, Raffaella; Del Amo, Yolanda; Denis, Michel; Dubelaar, George BJ; Endres, Sonja; Haraguchi, Lumi; Karlson, Bengt; Lambert, Christophe; Louchart, Arnaud; Marie, Dominique; Moncoiffé, Gwenaëlle; Pecqueur, David; Ribalet, François; Rijkeboer, Machteld; Silovic, Tina; Silva, Ricardo; Marro, Sophie; Sosik, Heidi M; Sourisseau, Marc; Tarran, Glen A; Van Oostende, Nicolas; Zhao, Li; Zheng, Shan (2022): Interoperable vocabulary for marine microbial flow cytometry. Frontiers in Marine Science, 9, 975877, https://doi.org/10.3389/fmars.2022.975877 Zubkov, M V; Burkill, P H; Topping, J N (2006): Flow cytometric enumeration of DNA-stained oceanic planktonic protists. Journal of Plankton Research, 29(1), 79-86, https://doi.org/10.1093/plankt/fbl059 https://doi.pangaea.de/10.1594/PANGAEA.963430 https://doi.org/10.1594/PANGAEA.963430 CC-BY-4.0: Creative Commons Attribution 4.0 International Access constraints: unrestricted info:eu-repo/semantics/openAccess Acoustic focusing cytometer Thermo Fisher Attune NxT [20 mW 488 nm (blue) laser] Activity description Arctic Arctic Ocean Cast number Collector CTD/Rosette CTD-RO DATE/TIME Depth bathymetric water Device type Event label Feature flow cytometry Flow cytometry system Becton Dickinson FACSCalibur HAVOC Heterotrophic nanophytoplankton Heterotrophic prokaryotes large medium very large Heterotrophic prokaryotes with relatively high nucleic acid Heterotrophic prokaryotes with relatively low nucleic acid LATITUDE Leg Number LONGITUDE microbial abundance MOSAiC MOSAiC_ECO MOSAiC20192020 MOSAiC expedition Multidisciplinary drifting Observatory for the Study of Arctic Climate Orange and red fluorescing nanophytoplankton Orange and red fluorescing picophytoplankton Orange fluorescing prokaryote picophytoplankton Polarstern PS122/1 PS122/1_10-44 PS122/1_7-49 PS122/1_8-46 dataset 2023 ftpangaea https://doi.org/10.1594/PANGAEA.96343010.5194/bg-5-523-200810.1128/AEM.65.1.45-52.199910.25607/OBP-1864.210.5281/zenodo.517973810.3389/fmars.2022.97587710.1093/plankt/fbl059 2024-09-18T00:10:44Z This dataset gives an overview of the abundance of microorganisms (smaller than 20 µm) enumerated using flow cytometry (FCM) during the Multidisciplinary drifting observatory for the study of Arctic Climate (MOSAiC) sampled from ship-based and on-ice CTD rosettes during leg 1, 2, 3, 4 and 5 (November 2019 – September 2020). Additional expedition and sampling details can be found in the ECO-overview paper (Fong et al., to be submitted to Elementa). We thank all persons involved in the expedition of the Research Vessel Polarstern during MOSAiC in 2019-2020 (AWI_PS122_00) as listed in Nixdorf et al. (2021). Flow cytometry (FCM) is a fast, high-throughput method to enumerate the abundance of microorganism (smaller than 20 µm). FCM uses the hydrodynamic focusing of a laminar flow to separate and line up microscopic particles. When particles pass a laser beam, the generated light scattering can be used to estimate their cell size, obtain information about cell granularity and surface characteristics and determine fluorescence from inherent pigments or applied stains, such as DNA binding ones. Photosynthetic microorganisms have auto-fluorescent pigments, such as chlorophylls which in combination with the light scattering properties (cell size) or surface properties, can be used to group them into clusters of similar or identical organism types. Heterotrophic microorganisms, including archaea, bacteria and heterotrophic nanoflagellates, and virus do not have fluorescent pigments and require staining, for example using SYBR Green to stain Nucleic Acids (DNA/RNA) in order to distinguish these cells from other organic and inorganic particles in the sample. Samples for flow cytometric analysis were taken in triplicates or quadruplicates of 1.8 mL of sample water and fixed with 36 μL 25 % glutaraldehyde (0.5 % final concentration) at 4 °C in the dark for approximately 2 hours, then flash frozen in liquid nitrogen and stored at -80 °C until analysis. The abundance of pico- and nano-sized phytoplankton and heterotrophic ... Dataset Arctic Arctic Ocean Phytoplankton PANGAEA - Data Publisher for Earth & Environmental Science Arctic Arctic Ocean ENVELOPE(-35.676758,121.007309,89.072990,79.205856) |