http://lod.bco-dmo.org/id/dataset/739353
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
2018-06-27
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Plankton cell abundances and APA data from RV Atlantic Explorer BATS cruise BV50 in the North Atlantic subtropical gyre during September 2015.
2018-06-27
publication
2018-06-27
revision
BCO-DMO Linked Data URI
2018-06-27
creation
http://lod.bco-dmo.org/id/dataset/739353
Solange Duhamel
Lamont-Doherty Earth Observatory
principalInvestigator
Dr O. Roger Anderson
Lamont-Doherty Earth Observatory
principalInvestigator
Eunsoo Kim
American Museum of Natural History
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., Anderson, O. R., Kim, E. (2018) Plankton cell abundances and APA data from RV Atlantic Explorer BATS cruise BV50 in the North Atlantic subtropical gyre during September 2015. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2018-06-27 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/739353 [access date]
Plankton cell abundances and APA data. Dataset Description: <p>Plankton cell abundances and APA data collected on BV50 in the&nbsp;North Atlantic subtropical gyre&nbsp;(September 2015),&nbsp;along a transect from Bermuda to Puerto Rico extending from 33°N to 22°N.</p> Methods and Sampling: <p><strong>Flow cytometry analyses</strong></p>
<p>Duplicate 1.8-ml samples were fixed with paraformaldehyde (electron microscopy grade, 0.25% final concentration) for 15–20 min in the dark at room temperature, flash frozen in liquid nitrogen and preserved at -80°C until analysis. The sheath fluid consisted in a sodium chloride solution filtered in-line through a 0.22 µm Sterivex filter unit. Reference beads (Fluoresbrite, YG, 1-µm) were added to each sample to maintain proper alignment and focus of the instrument. <em>Prochlorococcus</em>, <em>Synechococcus</em> and pigmented protists (P-Protists) were discriminated in unstained samples based on their chlorophyll (red) fluorescence and forward scatter (FSC, size) signatures. The high phycoerythrin (orange) signal in <em>Synechococcus</em> was used to distinguish them from <em>Prochlorococcus</em> and P-Protists. Using a forward scatter detector with small particle option and focusing a 488 plus a 457 nm (200 and 300 mW solid state, respectively) laser into the same pinhole permitted the resolution of dim surface <em>Prochlorococcus</em> group from background noise (Duhamel et al., 2014). Additionally, non-pigmented protists (NP-Protists) were discriminated from P-Protists in SYBR Green stained samples using a chlorophyll (red) vs SYBR Green (green) fluorescence plot, as described in Christaki et al. (2011) and Bock et al. (2018).</p>
<p><strong>Microscopy</strong></p>
<p>Ten-ml aliquots of the formalin-fixed plankton samples were centrifuged to sediment the plankton, and the overlying supernatant removed leaving 0.5 to 1 ml. The sedimented pellet was gently resuspended in the remaining supernatant and stained with Lugol’s iodine. Samples of the thoroughly suspended stained sample (20 µl) were taken with a micropipette and deposited as a droplet in the base of an Uttermohl viewing chamber and examined using an inverted compound microscope with phase contrast optics. The contents of each 20-µl droplet was scanned field-by-field exhaustively at 400x, and each individual microplankton observed was measured in the micron range, using an ocular reticule, and assigned to a broad taxonomic morphogroup (e.g., coccolithophore, diatom, dinoflatellate). Examples of individuals within each morphogroup were photographed using a digital camera, and representative images of each morphogroup were assembled in a plate of micrographs illustrating the range of microplankton that were observed.</p>
<p><strong>Alkaline phosphatase activity </strong></p>
<p>Alkaline phosphatase activity (APA) was measured following a modification of the Dyhrman and Ruttenberg (2006) protocol. Seawater samples were collected onto two separate filters with 0.2- and 0.8-µm porosities, chosen to tease apart activity by the bacterioplankton (i.e. bacteria and cyanobacteria) and the protists enriched fractions (0.2–0. 8 μm and &gt;0.8 µm, respectively). Filters were stored frozen at –20°C until analysis (&lt;1 month). Samples were processed using the fluorogenic phosphatase substrate 4-methylumbelliferyl phosphate (MUF-P, Sigma-Aldrich) at saturating concentration (10 μmol l<sup>–1</sup>, Casey et al. (2009)). Fluorescence was measured at several time points within the linear range of the assay. A standard curve using 4-methylumbelliferone (MUF, Sigma-Aldrich) was used to calculate MUF-P hydrolysis rates (Duhamel et al 2011).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1458070 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1458070
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
Dr O. Roger Anderson
Lamont-Doherty Earth Observatory
845-365-8452
Biology and Paleoenvironment Division 61 Route 9W - Marine Biology
Palisades
NY
10964-8000
USA
ora@ldeo.columbia.edu
pointOfContact
Eunsoo Kim
American Museum of Natural History
212-769-5975
Central Park West at 79th St
New York
NY
10024-5192
USA
ekim1@amnh.org
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Stn
Lat
Long
Pro
Syn
P_Prot
NP_Prot
Phyto
Dino
APA_0_2_0_8
APA_greaterThan_0_8
Cruise
BD Influx flow cytometer
Horiba FluoroMax-4 spectrofluorometer
Nikon Diaphot inverted compound microscope
theme
None, User defined
station
latitude
longitude
prochlorococcus abundance
synechococcus abundance
cell_concentration
alkaline phosphatase
Cruise identfier
featureType
BCO-DMO Standard Parameters
Flow Cytometer
Fluorometer
Inverted Microscope
instrument
BCO-DMO Standard Instruments
AE1524
service
Deployment Activity
North Atlantic subtropical gyre
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.
Collaborative Research: Role of small-sized protists in the microbial loop with emphasis on interactions between mixotrophic protists and picocyanobacteria
https://osprey.bco-dmo.org/project/542308
Collaborative Research: Role of small-sized protists in the microbial loop with emphasis on interactions between mixotrophic protists and picocyanobacteria
<p>This project is an NSF Collaborative Research Project.</p>
<p><em>Description from NSF award abstract:</em><br />
Protists are mostly single-celled, eukaryotic microorganisms, including algae and protozoans. They are ubiquitous, diverse, and major contributors in oceanic food webs. Determining their taxonomic identity and the extent to which they contribute to carbon and nutrient cycles (whereby carbon and minerals are continuously changed chemically in the environment and reincorporated in living organisms) are among the major goals of this study. Moreover, the investigators will study how they respond to environmental change, one of the most important and challenging current problems in oceanography. Answering these questions is fundamental to understanding how living organisms in the ocean environment interact with one another and contribute to the health and productivity of the ocean. The main goal of the project is to investigate biotic interactions of small-sized protists with very tiny cyanobacteria also known as picocyanobacteria, which represent the most abundant photosynthetic organisms in the ocean. These studies will be done both in ocean environments and in laboratory experimental settings. Considering the limited knowledge on this topic, the work planned in this project promises important and exciting discoveries. Two early career female scientists will lead this project. In addition, one postdoctoral scholar, one graduate student, and at least three undergraduate summer interns will participate in the proposed research activities. The principal investigators will create a strong public outreach program that will engage middle school students in hands-on activities related to ocean sciences, and will produce a video in collaboration with the Education Department at the American Museum of Natural History. The video will summarize the major findings of the proposed research. It can be used in schools and in informal learning settings, including access by the public on the Internet through the Museum's Science Bulletins web page.</p>
<p>Single-celled eukaryotic microorganisms or protists, though largely outnumbered by picocyanobacteria (<em>Prochlorococcus</em> and <em>Synechococcus</em>), contribute significantly to ocean carbon biomass and primary productivity, partially by virtue of their larger cell size. In addition, small planktonic protists can regulate picocyanobacteria abundance through grazing. The main goal of this project is to investigate biotic interactions of planktonic pico- and nano-sized eukaryotes with picocyanobacteria, both in the field and in laboratory settings. A set of field- and culture-based experiments will be conducted, using state-of-the-art methodologies, including fluorescence-activated cell sorting, isotope and fluorescent stain labeling, and next-generation molecular sequencing to address the research objectives.</p>
<p>Operationally, this project is structured around two objectives:</p>
<p>Objective 1 is to assess the contribution of small protists to carbon and nutrient cycling through measurement of primary production, bacterivory, mixotrophy and phosphorus uptake in major microbial groups, and evaluate the role of nutrient availability in controlling mixotrophy.</p>
<p>Objective 2 will focus on assessing the distribution and diversity of small-sized protists that feed on picocyanobacteria and further evaluate the role of nutrient availability among the protists that are mixotrophic.</p>
<p>To reach these objectives field-based experiments will be conducted in contrasted environments: the North Pacific subtropical gyre (phosphorus replete, dominated by <em>Prochlorococcus</em> at Sta. ALOHA) and the North West Mediterranean sea (phosphorus deplete, dominated by <em>Synechococcu</em>s at Sta. DYFAMED). Complementary experiments using model protists and picocyanobacteria will be conducted using controlled cultures in the lab. The work will provide critical new information on the phylogenetic diversity and function of marine microbial eukaryotes, with emphasis on their ecological role as predators (phagotrophy, mixotrophy) on, and competitors with, the picoyanobacteria<em> Prochlorococcus</em> and <em>Synechococcus</em>.</p>
Small protists in microbial loop
largerWorkCitation
project
eng; USA
oceans
North Atlantic subtropical gyre
-66.2052
-63.2169
21.8378
33.4468
2015-09-24
2015-09-29
North Pacific subtropical gyre (Station ALOHA) and Northwestern Mediterranean Sea (Station DYFAMED)
0
BCO-DMO catalogue of parameters from Plankton cell abundances and APA data from RV Atlantic Explorer BATS cruise BV50 in the North Atlantic subtropical gyre during September 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/743160.rdf
Name: Stn
Units: unitless
Description: <p>Station number</p>
http://lod.bco-dmo.org/id/dataset-parameter/743161.rdf
Name: Lat
Units: decimal degrees
Description: <p>Latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/743162.rdf
Name: Long
Units: decimal degrees
Description: <p>Longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/743163.rdf
Name: Pro
Units: x10^3 cell per milliliter
Description: <p>Prochlorococcus cell abundance</p>
http://lod.bco-dmo.org/id/dataset-parameter/743164.rdf
Name: Syn
Units: x10^3 cell per milliliter
Description: <p>Synechococcus cell abundance</p>
http://lod.bco-dmo.org/id/dataset-parameter/743165.rdf
Name: P_Prot
Units: x10^3 cell per milliliter
Description: <p>Pigmented protist cell abundance</p>
http://lod.bco-dmo.org/id/dataset-parameter/743166.rdf
Name: NP_Prot
Units: x10^3 cell per milliliter
Description: <p>Non-Pigmented protist cell abundance</p>
http://lod.bco-dmo.org/id/dataset-parameter/743167.rdf
Name: Phyto
Units: x10^3 cell per liter
Description: <p>Phytoplankton cell abundance</p>
http://lod.bco-dmo.org/id/dataset-parameter/743168.rdf
Name: Dino
Units: x10^3 cell per liter
Description: <p>Dinoflagellate cell abundance</p>
http://lod.bco-dmo.org/id/dataset-parameter/743169.rdf
Name: APA_0_2_0_8
Units: nmol L -1 h -1
Description: <p>Alkaline phosphatase activity in the 0.2 to 0.8 um size fraction</p>
http://lod.bco-dmo.org/id/dataset-parameter/743170.rdf
Name: APA_greaterThan_0_8
Units: nmol L -1 h -1
Description: <p>Alkaline phosphatase activity in the size fraction greater than 0.8 um</p>
http://lod.bco-dmo.org/id/dataset-parameter/743173.rdf
Name: Cruise
Units: unitless
Description: <p>Cruise ID</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
352
https://datadocs.bco-dmo.org/file/g77yOn1sPNxkl7/BV50_cell.csv
BV50_cell.csv
Primary data file for dataset ID 739353
download
https://osprey.bco-dmo.org/dataset/739353/data/download
download
onLine
dataset
<p><strong>Flow cytometry analyses</strong></p>
<p>Duplicate 1.8-ml samples were fixed with paraformaldehyde (electron microscopy grade, 0.25% final concentration) for 15–20 min in the dark at room temperature, flash frozen in liquid nitrogen and preserved at -80°C until analysis. The sheath fluid consisted in a sodium chloride solution filtered in-line through a 0.22 µm Sterivex filter unit. Reference beads (Fluoresbrite, YG, 1-µm) were added to each sample to maintain proper alignment and focus of the instrument. <em>Prochlorococcus</em>, <em>Synechococcus</em> and pigmented protists (P-Protists) were discriminated in unstained samples based on their chlorophyll (red) fluorescence and forward scatter (FSC, size) signatures. The high phycoerythrin (orange) signal in <em>Synechococcus</em> was used to distinguish them from <em>Prochlorococcus</em> and P-Protists. Using a forward scatter detector with small particle option and focusing a 488 plus a 457 nm (200 and 300 mW solid state, respectively) laser into the same pinhole permitted the resolution of dim surface <em>Prochlorococcus</em> group from background noise (Duhamel et al., 2014). Additionally, non-pigmented protists (NP-Protists) were discriminated from P-Protists in SYBR Green stained samples using a chlorophyll (red) vs SYBR Green (green) fluorescence plot, as described in Christaki et al. (2011) and Bock et al. (2018).</p>
<p><strong>Microscopy</strong></p>
<p>Ten-ml aliquots of the formalin-fixed plankton samples were centrifuged to sediment the plankton, and the overlying supernatant removed leaving 0.5 to 1 ml. The sedimented pellet was gently resuspended in the remaining supernatant and stained with Lugol’s iodine. Samples of the thoroughly suspended stained sample (20 µl) were taken with a micropipette and deposited as a droplet in the base of an Uttermohl viewing chamber and examined using an inverted compound microscope with phase contrast optics. The contents of each 20-µl droplet was scanned field-by-field exhaustively at 400x, and each individual microplankton observed was measured in the micron range, using an ocular reticule, and assigned to a broad taxonomic morphogroup (e.g., coccolithophore, diatom, dinoflatellate). Examples of individuals within each morphogroup were photographed using a digital camera, and representative images of each morphogroup were assembled in a plate of micrographs illustrating the range of microplankton that were observed.</p>
<p><strong>Alkaline phosphatase activity </strong></p>
<p>Alkaline phosphatase activity (APA) was measured following a modification of the Dyhrman and Ruttenberg (2006) protocol. Seawater samples were collected onto two separate filters with 0.2- and 0.8-µm porosities, chosen to tease apart activity by the bacterioplankton (i.e. bacteria and cyanobacteria) and the protists enriched fractions (0.2–0. 8 μm and &gt;0.8 µm, respectively). Filters were stored frozen at –20°C until analysis (&lt;1 month). Samples were processed using the fluorogenic phosphatase substrate 4-methylumbelliferyl phosphate (MUF-P, Sigma-Aldrich) at saturating concentration (10 μmol l<sup>–1</sup>, Casey et al. (2009)). Fluorescence was measured at several time points within the linear range of the assay. A standard curve using 4-methylumbelliferone (MUF, Sigma-Aldrich) was used to calculate MUF-P hydrolysis rates (Duhamel et al 2011).</p>
Specified by the Principal Investigator(s)
<p>For cell enumeration, cytograms were analyzed using FCS Express 6 Flow Cytometry Software (De Novo Software, CA, US). Data were analyzed using MS Excel.</p>
<p><strong>BCO-DMO Data Processing Notes:</strong></p>
<p>-Changed N.D. to nd<br />
-Reformatted column names to meet BCO-DMO standards<br />
-Changed points in column names to underscores<br />
-Added Cruise column</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
BD Influx flow cytometer
BD Influx flow cytometer
PI Supplied Instrument Name: BD Influx flow cytometer PI Supplied Instrument Description:Used for flow cytometry analyses 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/
Horiba FluoroMax-4 spectrofluorometer
Horiba FluoroMax-4 spectrofluorometer
PI Supplied Instrument Name: Horiba FluoroMax-4 spectrofluorometer PI Supplied Instrument Description:Used to measure fluorescence Instrument Name: Fluorometer Instrument Short Name:Fluorometer Instrument Description: A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/113/
Nikon Diaphot inverted compound microscope
Nikon Diaphot inverted compound microscope
PI Supplied Instrument Name: Nikon Diaphot inverted compound microscope PI Supplied Instrument Description:Used in microscopy analyses Instrument Name: Inverted Microscope Instrument Short Name: Instrument Description: An inverted microscope is a microscope with its light source and condenser on the top, above the stage pointing down, while the objectives and turret are below the stage pointing up. It was invented in 1850 by J. Lawrence Smith, a faculty member of Tulane University (then named the Medical College of Louisiana).
Inverted microscopes are useful for observing living cells or organisms at the bottom of a large container (e.g. a tissue culture flask) under more natural conditions than on a glass slide, as is the case with a conventional microscope. Inverted microscopes are also used in micromanipulation applications where space above the specimen is required for manipulator mechanisms and the microtools they hold, and in metallurgical applications where polished samples can be placed on top of the stage and viewed from underneath using reflecting objectives.
The stage on an inverted microscope is usually fixed, and focus is adjusted by moving the objective lens along a vertical axis to bring it closer to or further from the specimen. The focus mechanism typically has a dual concentric knob for coarse and fine adjustment. Depending on the size of the microscope, four to six objective lenses of different magnifications may be fitted to a rotating turret known as a nosepiece. These microscopes may also be fitted with accessories for fitting still and video cameras, fluorescence illumination, confocal scanning and many other applications. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB05/
Cruise: AE1524
AE1524
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel