http://lod.bco-dmo.org/id/dataset/517419
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
2014-06-24
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Cell abundance estimates of heterotrophic protists by size-class, based on epifluorescence microscopy from samples collected on R/V Melville cruise MV1008 in the Costa Rica Dome in 2010 (CRD FLUZiE project)
2014-06-24
publication
2014-06-24
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2019-12-30
publication
https://doi.org/10.1575/1912/bco-dmo.517419.1
Michael R. Landry
University of California-San Diego Scripps
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: Landry, M. (2014) Cell abundance estimates of heterotrophic protists by size-class, based on epifluorescence microscopy from samples collected on R/V Melville cruise MV1008 in the Costa Rica Dome in 2010 (CRD FLUZiE project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2014-06-24 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.517419.1 [access date]
Cell abundance estimates of heterotrophic protists by size-class, based on epifluorescence microscopy. Dataset Description: <p>Cell abundance estimates of heterotrophic protists by size-class, based on epifluorescence microscopy. Samples were collected on the MV1008 cruise in the Costa Rica Dome (CRD) region of the Eastern Tropical Pacific Ocean.</p> Methods and Sampling: <p>Seawater samples (500 mL) for microscopical analysis were gently collected from the CTD and immediately preserved for slide preparation according to a modified protocol of Sherr and Sherr (1993). The samples were first preserved with 260 uL of alkaline Lugol’s solution, immediately followed by 10 mL of buffered formalin and 500 uL of sodium thiosulfate, with gentle mixing between each addition. Preserved samples were shielded from light and left to rest at room temperature for 1 h. After the rest period, 1 mL of proflavin (0.33% w/v) was added and the samples were stored in the dark for an additional hour. Just prior to filtration, the preserved samples were stained with 1 mL of DAPI (0.01 mg mL<sup>-1</sup>) and immediately transferred to the filtration manifold. A 50-mL aliquot (small volume, SV) of the sample was filtered through a 25-mm black polycarbonate filter with 0.8-um pore size, and the remaining 450 mL aliquot (large volume, LV) was filtered through a 25-mm black polycarbonate filter with 8.0-um pores. A 10-mm nylon backing filter was placed under all polycarbonate filters to promote even cell distribution, and filtered the samples under gentle vacuum pressure (&lt;100 mm Hg). Each filter was then mounted onto glass slides with one drop of Type DF immersion oil and a No. 2 cover slip, and the prepared slides were frozen at -80°C for later analysis in the lab. NOTE: ciliated protists are poorly preserved by this method and are not included in these analyses.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0826626 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0826626
completed
Michael R. Landry
University of California-San Diego Scripps
858-534-4702
9500 Gilman Drive Mail Code: 0227
La Jolla
CA
92093-0227
USA
mlandry@ucsd.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
event
cast
cycle
date_local
lat
lon
depth
niskin
taxon
size_class
abundance
Zeiss AxioCam MRc
Zeiss Axiovert 200 M inverted compound microscope
theme
None, User defined
event
cast
No BCO-DMO term
date
latitude
longitude
depth
Niskin bottle number
taxon
abundance
featureType
BCO-DMO Standard Parameters
Camera
Inverted Microscope
instrument
BCO-DMO Standard Instruments
MV1008
service
Deployment Activity
Costa Rica Dome
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.
Integrated Marine Biogeochemistry and Ecosystem Research -US
http://www.imber.info/
Integrated Marine Biogeochemistry and Ecosystem Research -US
The BCO-DMO database includes data from IMBER endorsed projects lead by US funded investigators. There is no dedicated US IMBER project or data management office. Those functions are provided by US-OCB and BCO-DMO respectively.
The information in this program description pertains to the Internationally coordinated IMBER research program. The projects contributing data to the BCO-DMO database are those funded by US NSF only. The full IMBER data catalog is hosted at the Global Change Master Directory (GCMD).
IMBER Data Portal: The IMBER project has chosen to create a metadata portal hosted by the NASA's Global Change Master Directory (GCMD). The GCMD IMBER data catalog provides an overview of all IMBER endorsed and related projects and links to datasets, and can be found at URL http://gcmd.nasa.gov/portals/imber/.
IMBER research will seek to identify the mechanisms by which marine life influences marine biogeochemical cycles, and how these, in turn, influence marine ecosystems. Central to the IMBER goal is the development of a predictive understanding of how marine biogeochemical cycles and ecosystems respond to complex forcings, such as large-scale climatic variations, changing physical dynamics, carbon cycle chemistry and nutrient fluxes, and the impacts of marine harvesting. Changes in marine biogeochemical cycles and ecosystems due to global change will also have consequences for the broader Earth System. An even greater challenge will be drawing together the natural and social science communities to study some of the key impacts and feedbacks between the marine and human systems.
To address the IMBER goal, four scientific themes, each including several issues, have been identified for the IMBER project: Theme 1 - Interactions between Biogeochemical Cycles and Marine Food Webs; Theme 2 - Sensitivity to Global Change: How will key marine biogeochemical cycles, ecosystems and their interactions, respond to global change?; Theme 3 - Feedback to the Earth System: What are the roles of the ocean biogeochemistry and ecosystems in regulating climate?; and Theme 4 - Responses of Society: What are the relationships between marine biogeochemical cycles, ecosystems, and the human system?
IMBER-US
largerWorkCitation
program
Ocean Carbon and Biogeochemistry
http://us-ocb.org/
Ocean Carbon and Biogeochemistry
The Ocean Carbon and Biogeochemistry (OCB) program focuses on the ocean's role as a component of the global Earth system, bringing together research in geochemistry, ocean physics, and ecology that inform on and advance our understanding of ocean biogeochemistry. The overall program goals are to promote, plan, and coordinate collaborative, multidisciplinary research opportunities within the U.S. research community and with international partners. Important OCB-related activities currently include: the Ocean Carbon and Climate Change (OCCC) and the North American Carbon Program (NACP); U.S. contributions to IMBER, SOLAS, CARBOOCEAN; and numerous U.S. single-investigator and medium-size research projects funded by U.S. federal agencies including NASA, NOAA, and NSF.
The scientific mission of OCB is to study the evolving role of the ocean in the global carbon cycle, in the face of environmental variability and change through studies of marine biogeochemical cycles and associated ecosystems.
The overarching OCB science themes include improved understanding and prediction of: 1) oceanic uptake and release of atmospheric CO2 and other greenhouse gases and 2) environmental sensitivities of biogeochemical cycles, marine ecosystems, and interactions between the two.
The OCB Research Priorities (updated January 2012) include: ocean acidification; terrestrial/coastal carbon fluxes and exchanges; climate sensitivities of and change in ecosystem structure and associated impacts on biogeochemical cycles; mesopelagic ecological and biogeochemical interactions; benthic-pelagic feedbacks on biogeochemical cycles; ocean carbon uptake and storage; and expanding low-oxygen conditions in the coastal and open oceans.
OCB
largerWorkCitation
program
Costa Rica Dome FLUx and Zinc Experiments
https://osprey.bco-dmo.org/project/515387
Costa Rica Dome FLUx and Zinc Experiments
<p>Research was aimed at improved understanding of plankton dynamics, carbon and nutrient fluxes, and potential trace element limitation in the Costa Rica Dome region of the eastern tropical Pacific. The specific science objectives of the 2010 R/V Melville cruise (MV1008) were:<br />
1) to assess grazing and trace metal/nutrient controls on primary production and phytoplankton standing stocks;<br />
2) to quantify carbon and elemental fluxes and export rates from the euphotic zone; and<br />
3) to measure microbial population, processes, stable isotope abundances associated with the OMZ and nitrite maxima.</p>
<p>Additional information about MV1008 can be found in the <a href="http://dmoserv3.whoi.edu/data_docs/CRD_FLUZiE/CRUISE_REPORT_Melville1008.pdf" target="_blank">cruise report</a> (PDF).</p>
<p><strong>NOTE: </strong>The original proposal and award abstract are not relevant. The project was originally funded by NSF as experimental tests of phytoplankton controls in the Arabian Sea. Piracy concerns in the region led to the cancellation of the research cruise in 2009, and a Change of Scope request was approved to focus the project on related issues in the Costa Rica Dome (CRD).</p>
<p>Though this project is not formally affiliated with any large program, it aligns with IMBER's emphasis on community ecology and biogeochemistry, and the OCB focus on carbon-based measurements of production, grazing and export processes.</p>
CRD FLUZiE
largerWorkCitation
project
eng; USA
oceans
Costa Rica Dome
-92.98714
-89.99424
8.39218
10.29979
2010-07-04
2010-07-19
Costa Rica Dome, Eastern Tropical Pacific Ocean
0
BCO-DMO catalogue of parameters from Cell abundance estimates of heterotrophic protists by size-class, based on epifluorescence microscopy from samples collected on R/V Melville cruise MV1008 in the Costa Rica Dome in 2010 (CRD FLUZiE 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
http://lod.bco-dmo.org/id/dataset-parameter/517425.rdf
Name: event
Units: integer
Description: <p>Number referring to the particular activity (event) on the FluZiE cruise.</p>
http://lod.bco-dmo.org/id/dataset-parameter/517426.rdf
Name: cast
Units: integer
Description: <p>CTD Cast number from the FluZiE cruise.</p>
http://lod.bco-dmo.org/id/dataset-parameter/517427.rdf
Name: cycle
Units: text
Description: <p>Type and number of cruise sampling event. Either "Stn_n" or "Cycle_n". A transect of stations was sampled from 29 June to 03 July. Five quasi-Lagrangian experiments called "cycles" were conducted during the remainder of the cruise.</p>
http://lod.bco-dmo.org/id/dataset-parameter/517428.rdf
Name: date_local
Units: unitless
Description: <p>Date of CTD cast (local time zone of UTC -6). in the format mmddyyyy</p>
http://lod.bco-dmo.org/id/dataset-parameter/517429.rdf
Name: lat
Units: decimal degrees
Description: <p>Latitude in degrees North.</p>
http://lod.bco-dmo.org/id/dataset-parameter/517430.rdf
Name: lon
Units: decimal degrees
Description: <p>Longitude in degrees East.</p>
http://lod.bco-dmo.org/id/dataset-parameter/517431.rdf
Name: depth
Units: meters
Description: <p>Sample depth.</p>
http://lod.bco-dmo.org/id/dataset-parameter/517432.rdf
Name: niskin
Units: integer
Description: <p>Niskin bottle that the sample was taken from.</p>
http://lod.bco-dmo.org/id/dataset-parameter/517433.rdf
Name: taxon
Units: text
Description: <p>Taxon. heterotrophic_dinos = Heterotrophic Dinoflagellates; heterotrophic_flags = Heterotrophic Flagellates; all = all taxonomic groups (heterotrophic dinoflagellates + heterotrophic flagellates)</p>
http://lod.bco-dmo.org/id/dataset-parameter/517434.rdf
Name: size_class
Units: micrometers (um)
Description: <p>Size-Class Distribution (cell lengths are longest major axis): lt2 = cells < 2 um; 2_to_10 = cells 2-10 um; 10_to_20 = cells 10-20 um; gt20 = cells > 20 um; total = all sizes.</p>
http://lod.bco-dmo.org/id/dataset-parameter/517435.rdf
Name: abundance
Units: cells per milliliter (cells/mL)
Description: <p>Abundance of the taxon size class.</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
96761
https://darchive.mblwhoilibrary.org/bitstream/1912/25080/1/dataset-517419_microzooepiabund__v1.tsv
download
https://doi.org/10.1575/1912/bco-dmo.517419.1
download
onLine
dataset
<p>Seawater samples (500 mL) for microscopical analysis were gently collected from the CTD and immediately preserved for slide preparation according to a modified protocol of Sherr and Sherr (1993). The samples were first preserved with 260 uL of alkaline Lugol’s solution, immediately followed by 10 mL of buffered formalin and 500 uL of sodium thiosulfate, with gentle mixing between each addition. Preserved samples were shielded from light and left to rest at room temperature for 1 h. After the rest period, 1 mL of proflavin (0.33% w/v) was added and the samples were stored in the dark for an additional hour. Just prior to filtration, the preserved samples were stained with 1 mL of DAPI (0.01 mg mL<sup>-1</sup>) and immediately transferred to the filtration manifold. A 50-mL aliquot (small volume, SV) of the sample was filtered through a 25-mm black polycarbonate filter with 0.8-um pore size, and the remaining 450 mL aliquot (large volume, LV) was filtered through a 25-mm black polycarbonate filter with 8.0-um pores. A 10-mm nylon backing filter was placed under all polycarbonate filters to promote even cell distribution, and filtered the samples under gentle vacuum pressure (&lt;100 mm Hg). Each filter was then mounted onto glass slides with one drop of Type DF immersion oil and a No. 2 cover slip, and the prepared slides were frozen at -80°C for later analysis in the lab. NOTE: ciliated protists are poorly preserved by this method and are not included in these analyses.</p>
Specified by the Principal Investigator(s)
<p>Slides were digitally imaged using a Zeiss Axiovert 200 M inverted compound microscope equipped for high-throughput epifluorescence microscopy with a motorized focus drive, stage, objective and filters. Digital images were acquired with a Zeiss AxioCam MRc black and white 8-bit CCD camera. SV samples (50 mL aliquots) were viewed at 630X magnification, and LV samples (450 mL aliquots) were viewed at 200X magnification. A minimum of 20 random positions were imaged for each slide, with each position consisting of three to four fluorescent channels: Chl <em>a</em>, DAPI, FITC (SV and LV samples) and phycoerythrin (SV samples only). &nbsp;</p>
<p>Images were analyzed using ImagePro software to semi-automate the enumeration of eukaryotic cells larger than 1.5 um in length (Taylor et al., 2012). Whenever possible, 20 positions and &gt;300 cells were counted for each slide. Each cell was manually identified and grouped into identifiable taxonomic groups. Heterotrophic cells were distinguished from autotrophs (eukaryotic phytoplankton) by very low red autofluorescence (low/absent chlorophyll and absence of defined chloroplasts). Cells with recently consumed autotrophic prey were counted as heterotrophs.</p>
<p>BCO-DMO Processing Notes:<br />
- size_class and taxon columns were transposed from columns into rows.</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
Zeiss AxioCam MRc
Zeiss AxioCam MRc
PI Supplied Instrument Name: Zeiss AxioCam MRc PI Supplied Instrument Description:Digital images were acquired with a Zeiss AxioCam MRc black and white 8-bit CCD camera. Instrument Name: Camera Instrument Short Name:camera Instrument Description: All types of photographic equipment including stills, video, film and digital systems. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/311/
Zeiss Axiovert 200 M inverted compound microscope
Zeiss Axiovert 200 M inverted compound microscope
PI Supplied Instrument Name: Zeiss Axiovert 200 M inverted compound microscope PI Supplied Instrument Description:Slides were digitally imaged using a Zeiss Axiovert 200 M inverted compound microscope equipped for high-throughput epifluorescence microscopy with a motorized focus drive, stage, objective and filters. 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: MV1008
MV1008
R/V Melville
Community Standard Description
International Council for the Exploration of the Sea
R/V Melville
vessel
MV1008
Michael R. Landry
University of California-San Diego Scripps
http://dmoserv3.whoi.edu/data_docs/CRD_FLUZiE/CRUISE_REPORT_Melville1008.pdf
Report describing MV1008
R/V Melville
Community Standard Description
International Council for the Exploration of the Sea
R/V Melville
vessel