http://lod.bco-dmo.org/id/dataset/663918
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
2016-11-03
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Flow cytometry cell counts obtained during the R/V L'Atalante OUTPACE cruise between New Caledonia and Tahiti from February to April 2015
2016-11-03
publication
2016-11-03
revision
BCO-DMO Linked Data URI
2016-11-03
creation
http://lod.bco-dmo.org/id/dataset/663918
Solange Duhamel
Lamont-Doherty Earth Observatory
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: Duhamel, S. (2016) Flow cytometry cell counts obtained during the R/V L'Atalante OUTPACE cruise between New Caledonia and Tahiti from February to April 2015. Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2016-11-03 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/663918 [access date]
Flow cytometry cell counts obtained during the OUTPACE cruise Dataset Description: <p>This dataset contains abundances of cyanobacteria (<em>Synechococcus</em>, and&nbsp;<em>Prochlorococcus</em>),&nbsp;picoalgae, non-pigmented picoplankton (bacteria), and heterotrophic protists acquired&nbsp;through flow cytometry. &nbsp;Latitude, longitude, timestamp, and sample depth are also included in this dataset. &nbsp;</p>
<p>Water samples were acquired during the Oligotrophy to UlTra-oligotrophy PACific Experiment (OUTPACE) cruise between New Caledonia and Tahiti from February to April 2015.</p> Methods and Sampling: <p><strong>Analytical procedure:</strong></p>
<p>Microbial cell abundances were determined using an Influx flow cytometer. Briefly, pigmented groups (Prochlorococcus,&nbsp;Synechococcus, and picoalgae) were enumerated in unstained samples by their chlorophyll and forward scatter signatures (Marie et al. 1999). The high phycoerythrin signal in&nbsp;Synechococcus&nbsp;was used to distinguish this group from&nbsp;Prochlorococcus&nbsp;and picoalgae.</p>
<p>To visualize non-pigmented picoplankton (bacteria) and heterotrophic protists, samples were stained with SYBR Green I DNA dye (SG, 1:10000 final concentration, for 10 min at 4C in the dark) (Zubkov et al. 2007, Christaki et al. 2011). Because bacteria and&nbsp;Prochlorococcus&nbsp;groups exhibit overlapping signal characteristics in surface samples after SG staining, the abundances of bacteria in surface samples were calculated by subtracting the&nbsp;Prochlorococcus&nbsp;abundance, determined in the unstained aliquot, from the total SG-stained group abundance. An internal standard of 1-um diameter fluorescent microspheres (Fluoresbrite, Polysciences) was added to each sample.</p>
<p><strong>Sampling and Analytical Methodology:&nbsp;</strong></p>
<p>Seawater samples were acquired from bottle samples collected by a CTD rosette during the OUTPACE cruise. 1.8 ml water samples were collected in duplicate, fixed with 0.25% (w/v) paraformaldehyde, flash frozen, and preserved at -80C. One of the duplicate samples was used to count phytoplankton (Prochlorococcus,&nbsp;Synechococcus, picoalgae), and the other was used to count bacteria and protists.</p>
<p>For pigmented groups (Prochlorococcus,&nbsp;Synechococcus, and picoalgae), cells were excited using a combination of two lasers (488+456 nm) focused into one pinhole; while for non-pigmented groups (bacteria and heterotrophic protists), cells were excited using the 488 nm laser only. For calibration, a solution of 1-um diameter fluorescent microspheres (Fluoresbrite, Polysciences) was used.</p>
<p><strong>References:&nbsp;</strong></p>
<p>Christaki U, Courties C, Massana R, Catala P, Lebaron P, Gasol JM, Zubkov MV (2011) Optimized routine flow cytometric enumeration of heterotrophic flagellates using SYBR Green I. Limnology and Oceanography-Methods 9:329-339.&nbsp;https://doi.org/10.4319/lom.2011.9.329</p>
<p>Marie D, Partensky F, Vaulot D, Brussaard C (1999) Enumeration of Phytoplankton, Bacteria, and Viruses in Marine Samples. Current Protocols in Cytometry:11.11.11-11.11.15.&nbsp;https://doi.org/10.1002/0471142956.cy1111s10</p>
<p>Zubkov M, Burkill PH, Topping JN (2007) Flow cytometric enumeration of DNA-stained oceanic planktonic protists. Journal of Plankton Research 29:79-86. &nbsp;https://doi.org/10.1093/plankt/fbl059</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1434916 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1434916
completed
Solange Duhamel
Lamont-Doherty Earth Observatory
520-621-6047
1007 E Lowell Street Life Sciences South 315
Tucson
AZ
85721
USA
duhamel@arizona.edu
pointOfContact
asNeeded
Unknown
cast
bottle
depth_w
lat
lon
pro
syn
peuk
bacteria
protists
ISO_DateTime_UTC
Sea-Bird CTD 9+
Influx Flow cytometer
theme
None, User defined
cast
bottle
depth
latitude
longitude
abundance
ISO_DateTime_UTC
featureType
BCO-DMO Standard Parameters
CTD Sea-Bird
Flow Cytometer
instrument
BCO-DMO Standard Instruments
OUTPACE
service
Deployment Activity
South west Pacific between New Caledonia and Tahiti
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.
Photoheterotrophy in unicellular cyanobacteria: ecological drivers and significance for marine biogeochemistry
https://osprey.bco-dmo.org/project/542285
Photoheterotrophy in unicellular cyanobacteria: ecological drivers and significance for marine biogeochemistry
<p><em>Description from NSF award abstract:</em><br />
Unicellular cyanobacteria are major contributors to primary production and carbon export in the open ocean. They also play an important role in the control of nutrient availability. The ability of these microbes to harvest light energy benefits a range of physiological functions, but the effect of light on their metabolism (other than for photosynthesis) is poorly known and controversial. This project will investigate the role of light in uptake of organic substrates (carbon and nutrients) by unicellular cyanobacteria and elucidate the importance of photoheterotrophy. The ability of these organisms to assimilate organic compounds and its modulation by light and nutrients will provide additional hints about the ecological success of unicellular cyanobacteria in the ocean. The proposed work will involve field experiments in the southwest Pacific Ocean, complemented by laboratory experiments in controlled cultures of ecologically relevant cyanobacteria. The study will employ innovative methods, including single cell assays and molecular tools that target individual cyanobacteria and evaluate their response to light for the assimilation of organic substrates. This research project will lead to an increased understanding of the microbial adaptations to light and nutrient gradients and the role these adaptations play in elemental cycling in oceanic habitats.</p>
<p>Unicellular cyanobacteria inhabit the surface ocean (generally <150 m deep), and use solar energy to compete for a limited supply of available nutrients. Therefore, they are expected to utilize light energy not only for photosynthesis but also to enhance their metabolism of dissolved organic compounds. Yet, the role of light in the uptake of organic compounds (both carbon and nutrients) and the importance of photoheterotrophy are still poorly understood. This proposal seeks to investigate the ecological drivers and significance of photoheterotrophy in the unicellular cyanobacteria <em>Prochlorococcus</em> and <em>Synechococcus</em>, the most abundant groups of primary producers in the ocean, and <em>Crocosphaera</em> an important nitrogen fixing organism. This proposal argues that adaptations to specific light regimes must shape spatiotemporal partitioning of resources among microbial groups in the ocean. Field experiments along a west-east transect in the southwest Pacific Ocean will cover a range of nutrient conditions and cyanobacterial abundances. Radioactive substrate incubations combined with flow cytometry cell sorting and microautoradiography paired to catalyzed reporter deposition fluorescence in situ hybridization (MICRO-CARD-FISH) will allow the separation of unicellular cyanobacteria from non-pigmented bacterioplankton and evaluation of their response to light for the uptake of different organic substrates. These experiments will be complemented by laboratory tests in controlled cultures of axenic strains representative of different ecologically relevant functional groups of cyanobacteria. Lastly, the capacity of the important nitrogen fixer <em>Crocosphaera watsonii </em>to feed on glucose will be tested, taking advantage of the sequenced genome of the representative strain WH8501 in targeting the expression of genes involved in glucose metabolism in situ.</p>
<p>Project investigators will participate in a Southwest Pacific cruise, the OUTPACE (Oligotrophy to UlTraoligotrophy PACific Experiment) expedition. The cruise will sample stations along a West-East transect between New Caledonia and Tahiti.</p>
<p>More information:<br />
* OUTPACE cruise (doi: <a href="http://dx.doi.org/10.17600/15000900" target="_blank">http://dx.doi.org/10.17600/15000900</a>)<br />
* OUTPACE website: <a href="https://outpace.mio.univ-amu.fr/?lang=en" style="color: rgb(0, 102, 153); box-sizing: border-box; margin: 0px; padding: 0px; background-color: transparent; text-decoration-line: none; border: 0px; font-style: inherit; font-variant: inherit; font-weight: inherit; font-stretch: inherit; font-size: inherit; line-height: inherit; font-family: inherit; vertical-align: baseline;">https://outpace.mio.univ-amu.fr/?lang=en</a></p>
Photoheterotrophy in unicellular cyanobacteria
largerWorkCitation
project
eng; USA
oceans
South west Pacific between New Caledonia and Tahiti
159.6432
-159.99
-22.0008
-17.997
2016-11-03
Southwest Pacific
0
BCO-DMO catalogue of parameters from Flow cytometry cell counts obtained during the R/V L'Atalante OUTPACE cruise between New Caledonia and Tahiti from February to April 2015
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/663923.rdf
Name: cast
Units: unitless
Description: <p>CTD cast number that acquired sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/663924.rdf
Name: bottle
Units: unitless
Description: <p>bottle number</p>
http://lod.bco-dmo.org/id/dataset-parameter/663925.rdf
Name: depth_w
Units: meters
Description: <p>depth of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/663926.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude of cast</p>
http://lod.bco-dmo.org/id/dataset-parameter/663927.rdf
Name: lon
Units: decimal degrees
Description: <p>longitude of cast; west is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/663928.rdf
Name: pro
Units: cells per milliliter
Description: <p>Prochlorococcus cell abundance</p>
http://lod.bco-dmo.org/id/dataset-parameter/663929.rdf
Name: syn
Units: cells per milliliter
Description: <p>Synechococcus cell abundance</p>
http://lod.bco-dmo.org/id/dataset-parameter/663930.rdf
Name: peuk
Units: cells per milliliter
Description: <p>picoalgae cell abundance</p>
http://lod.bco-dmo.org/id/dataset-parameter/663931.rdf
Name: bacteria
Units: cells per milliliter
Description: <p>non-pigmented pico plankton (bacteria) cell abundance</p>
http://lod.bco-dmo.org/id/dataset-parameter/663932.rdf
Name: protists
Units: cells per milliliter
Description: <p>heterotrophic (non-pigmented) protist cell abundance</p>
http://lod.bco-dmo.org/id/dataset-parameter/663951.rdf
Name: ISO_DateTime_UTC
Units: unitless
Description: <p> ISO formatted date/time (UTC) in format YYYY-mm-ddTHH:MM:SS[.xx]</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
32503
https://datadocs.bco-dmo.org/file/N77GgDZcNKxq2E/flowCyto.csv
flowCyto.csv
Primary data file for dataset ID 663918
download
https://osprey.bco-dmo.org/dataset/663918/data/download
download
onLine
dataset
<p><strong>Analytical procedure:</strong></p>
<p>Microbial cell abundances were determined using an Influx flow cytometer. Briefly, pigmented groups (Prochlorococcus,&nbsp;Synechococcus, and picoalgae) were enumerated in unstained samples by their chlorophyll and forward scatter signatures (Marie et al. 1999). The high phycoerythrin signal in&nbsp;Synechococcus&nbsp;was used to distinguish this group from&nbsp;Prochlorococcus&nbsp;and picoalgae.</p>
<p>To visualize non-pigmented picoplankton (bacteria) and heterotrophic protists, samples were stained with SYBR Green I DNA dye (SG, 1:10000 final concentration, for 10 min at 4C in the dark) (Zubkov et al. 2007, Christaki et al. 2011). Because bacteria and&nbsp;Prochlorococcus&nbsp;groups exhibit overlapping signal characteristics in surface samples after SG staining, the abundances of bacteria in surface samples were calculated by subtracting the&nbsp;Prochlorococcus&nbsp;abundance, determined in the unstained aliquot, from the total SG-stained group abundance. An internal standard of 1-um diameter fluorescent microspheres (Fluoresbrite, Polysciences) was added to each sample.</p>
<p><strong>Sampling and Analytical Methodology:&nbsp;</strong></p>
<p>Seawater samples were acquired from bottle samples collected by a CTD rosette during the OUTPACE cruise. 1.8 ml water samples were collected in duplicate, fixed with 0.25% (w/v) paraformaldehyde, flash frozen, and preserved at -80C. One of the duplicate samples was used to count phytoplankton (Prochlorococcus,&nbsp;Synechococcus, picoalgae), and the other was used to count bacteria and protists.</p>
<p>For pigmented groups (Prochlorococcus,&nbsp;Synechococcus, and picoalgae), cells were excited using a combination of two lasers (488+456 nm) focused into one pinhole; while for non-pigmented groups (bacteria and heterotrophic protists), cells were excited using the 488 nm laser only. For calibration, a solution of 1-um diameter fluorescent microspheres (Fluoresbrite, Polysciences) was used.</p>
<p><strong>References:&nbsp;</strong></p>
<p>Christaki U, Courties C, Massana R, Catala P, Lebaron P, Gasol JM, Zubkov MV (2011) Optimized routine flow cytometric enumeration of heterotrophic flagellates using SYBR Green I. Limnology and Oceanography-Methods 9:329-339.&nbsp;https://doi.org/10.4319/lom.2011.9.329</p>
<p>Marie D, Partensky F, Vaulot D, Brussaard C (1999) Enumeration of Phytoplankton, Bacteria, and Viruses in Marine Samples. Current Protocols in Cytometry:11.11.11-11.11.15.&nbsp;https://doi.org/10.1002/0471142956.cy1111s10</p>
<p>Zubkov M, Burkill PH, Topping JN (2007) Flow cytometric enumeration of DNA-stained oceanic planktonic protists. Journal of Plankton Research 29:79-86. &nbsp;https://doi.org/10.1093/plankt/fbl059</p>
from Cruise: OUTPACE <p>OUTPACE (Oligotrophy to UlTra-oligotrophy PACific Experiment) cruise onboard the RV L'Atalante (France) https://outpace.mio.univ-amu.fr/</p>
<p>OUTPACE cruise DOI: http://dx.doi.org/10.17600/15000900</p>
Specified by the Principal Investigator(s)
<p>Flow cytometry data were analyzed using FCS Express Pro (De Novo Software).&nbsp;</p>
<p>BCO-DMO Processing Notes:</p>
<p>* added ISO timestamp from OUTPACE cruise CTD logs&nbsp;<br />
* stripped out_c_ from station column for matching with bottle data&nbsp;<br />
* column station renamed cast to be consistent with CTD log<br />
* added a&nbsp;conventional&nbsp;header with dataset name, PI name, version date<br />
* modified parameter names to conform with BCO-DMO naming conventions</p>
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
Sea-Bird CTD 9+
Sea-Bird CTD 9+
PI Supplied Instrument Name: Sea-Bird CTD 9+ PI Supplied Instrument Description:This CTD-Rosette was called "classique" to differentiate it from the trace metal CTD-Rosette.
For more information on the CTD configuration see the OUTPACE site.
Instrument Name: CTD Sea-Bird Instrument Short Name:CTD Sea-Bird Instrument Description: A Conductivity, Temperature, Depth (CTD) sensor package from SeaBird Electronics. This instrument designation is used when specific make and model are not known or when a more specific term is not available in the BCO-DMO vocabulary. Refer to the dataset-specific metadata for more information about the specific CTD used. More information from: http://www.seabird.com/ Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/130/
Influx Flow cytometer
Influx Flow cytometer
PI Supplied Instrument Name: Influx Flow cytometer PI Supplied Instrument Description:Instrument Type: Flow cytometer (Manufacturer: BD) Model: Influx Instrument Name: Flow Cytometer Instrument Short Name:Flow Cytometer Instrument Description: Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells.
(from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm) Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB37/
Cruise: OUTPACE
OUTPACE
R/V L'Atalante
Community Standard Description
International Council for the Exploration of the Sea
R/V L'Atalante
vessel
OUTPACE
Thierry Moutin
Mediterranean Institute of Oceanography
R/V L'Atalante
Community Standard Description
International Council for the Exploration of the Sea
R/V L'Atalante
vessel