http://lod.bco-dmo.org/id/dataset/471609
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
2013-11-14
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Protist numbers at and below 100 m from R/V Pelagia 64PE280, 64PE325 in the tropical and subtropical N. Atlantic from 2007-2010 (Basin-scale Protists project)
2013-11-13
publication
2013-11-13
revision
BCO-DMO Linked Data URI
2013-11-13
creation
http://lod.bco-dmo.org/id/dataset/471609
Alexander Boris Bochdansky
Old Dominion University
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: Bochdansky, A. B. (2013) Protist numbers at and below 100 m from R/V Pelagia 64PE280, 64PE325 in the tropical and subtropical N. Atlantic from 2007-2010 (Basin-scale Protists project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2013-11-13 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/471609 [access date]
Protist numbers in subtropical North Atlantic at and below 100 m Dataset Description: Methods and Sampling: <p>Excerpt from Morgan-Smith et al. (2013):</p>
<p>Samples were collected using a rosette sampler fitted with 25 L Niskin bottles. Samples were immediately fixed with 0.2 micron-filtered methanol-stabilized formaldehyde (final concentration ~2%) and kept overnight at room temperature to allow outgassing and prevent bubble formation on filters. Subsamples of 100-250 ml were then filtered under gentle vacuum (-200mbar) onto Millipore 0.2 micron white polycarbonate filters for DAPI-FITC. A pore size of 0.2 micron is preferred for enumeration of total eukaryotes because some smaller eukaryotes are lost through the pores of 0.8 micron filters, leading to underestimation of eukaryote abundance (Morgan-Smith et al., 2011). Filters were washed with phosphate buffered saline (PBS) and ultra-pure water, then immediately stored at -80 C.</p>
<p>DAPI-FITC double staining was used to enumerate total eukaryotes. Pie-shaped slices of approximately 1/16-1/8 of filter were cut and 3-4 of these slices were placed atop a 25 mm diameter, 0.2 micron pore size polycarbonate filter on a glass frit and covered with a 10-ml filter tower, which was then flooded with 1ml FITC staining solution (2.5 ml 0.5 M sodium carbonate buffer, pH 9; 11 ml 0.01 M potassium phosphate buffer, pH 7.2; 11 ml 0.85 % sodium chloride; 10 mg FITC), and incubated for 10 min in the dark. Then vacuum was applied (-200 mbar) and filters were washed twice with 10 ml ice-cold carbonate buffer (0.5M, pH9). Filter sections were mounted on slides using Vectashield mounting medium with DAPI and stored at -20 C until analysis. Samples were counted on Olympus BX51 and BX50 epifluorescence micro scopes.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0826659 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0826659
completed
Alexander Boris Bochdansky
Old Dominion University
757-683-4933
Ocean, Earth and Atmospheric Sciences 4600 Elkhorn Ave.
Norfolk
VA
23529
USA
abochdan@odu.edu
pointOfContact
asNeeded
Unknown
cruise_id
cruise_name
sta
date
lat
lon
depth
vol
split
temp
sal
O2
FITC_2
FITC_8
EUK516
KIN516
LabY
PF2
Alv01
DiploR1792
NS4
Fluorescence Microscope
Niskin bottle
theme
None, User defined
Cruise identfier
cruise name
station
date
latitude
longitude
depth
No BCO-DMO term
water temperature at measurement depth
salinity
dissolved Oxygen
featureType
BCO-DMO Standard Parameters
Fluorescence Microscope
Niskin bottle
instrument
BCO-DMO Standard Instruments
64PE280
64PE325
service
Deployment Activity
Tropical and subtropical Atlantic
subtropical Atlantic
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
Basin-scale distribution and activity of deep-sea protists in the North Atlantic Ocean
https://osprey.bco-dmo.org/project/2290
Basin-scale distribution and activity of deep-sea protists in the North Atlantic Ocean
<p>ABSTRACT</p>
<p>Little is known about the distribution and ecology of eukaryotic microbes of the deep sea water column. Most of these microbes are small heterotrophic flagellates that feed on bacteria, where biomass in turn is fueled by the input of dissolved and particulate organic material from the surface. This study seeks to understand the distribution of eukaryotic microbes (i.e., protists) in the context of large, basin scale variations in hydrographic and chemical properties. The main hypothesis is that the abundance and taxonomic composition of protists serve as sensitive indicators of the strength and type (particulate or dissolved) of input of organic carbon into the deep ocean system. Samples in vertical profiles targeting major water masses across the North Atlantic will be collected. In addition, deep sea samples will be retrieved under pressure and incubated at in situ pressure and temperature in four newly designed chemostat systems. These cultures will be sub-sampled under pressure and examined for nutrient concentration, as well as for the purpose of monitoring the abundance of both prokaryotes and protists in the chambers. Using the same pressure samplers in short-term incubations, the investigators will explore the activity of deep sea protists by investigating the proportion of actively feeding organisms on fluorescently labeled bacteria. They will enumerate deep sea protists using a combination of fluorescence in situ hybridization and traditional staining methods, and will support taxonomic classifications using electron microscopy. Semi-automated epifluorescence microscopy with image analysis capabilities will be used to scan major filter areas and probe for rare microbes that normally fall below detection limits of other methods. In laboratory experiments, the investigators will use the newly built culture system to study pressure effects of eukaryotic protists while simulating temperature and pressure changes that sinking particles are exposed to when they sink to the abyss.<br />
</p>
Basin-scale Protists
largerWorkCitation
project
eng; USA
oceans
Tropical and subtropical Atlantic; subtropical Atlantic
2013-11-13
Tropical and subtropical Atlantic
0
BCO-DMO catalogue of parameters from Protist numbers at and below 100 m from R/V Pelagia 64PE280, 64PE325 in the tropical and subtropical N. Atlantic from 2007-2010 (Basin-scale Protists 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/471620.rdf
Name: cruise_id
Units: unitless
Description: cruise identification
http://lod.bco-dmo.org/id/dataset-parameter/471621.rdf
Name: cruise_name
Units: unitless
Description: alternate cruise name
http://lod.bco-dmo.org/id/dataset-parameter/471622.rdf
Name: sta
Units: unitless
Description: station number
http://lod.bco-dmo.org/id/dataset-parameter/471623.rdf
Name: date
Units: unitless
Description: UTC date
http://lod.bco-dmo.org/id/dataset-parameter/471624.rdf
Name: lat
Units: decimal degrees
Description: latitude
http://lod.bco-dmo.org/id/dataset-parameter/471625.rdf
Name: lon
Units: decimal degrees
Description: longitude
http://lod.bco-dmo.org/id/dataset-parameter/471626.rdf
Name: depth
Units: meters
Description: depth of sample
http://lod.bco-dmo.org/id/dataset-parameter/471627.rdf
Name: vol
Units: milliliters
Description: volume of water filtered onto 0.2 mm polycarbonate filters (25 mm diam.)
http://lod.bco-dmo.org/id/dataset-parameter/471628.rdf
Name: split
Units: cells
Description: <p>Epifluorescence counts of a specific nuclear morphotype as detectable with DAPI and described in Morgan-Smith et al. (2011) and Morgan-Smith et al. (2013). See references above</p>
http://lod.bco-dmo.org/id/dataset-parameter/471629.rdf
Name: temp
Units: degrees Celsius
Description: <p>temperature</p>
http://lod.bco-dmo.org/id/dataset-parameter/471630.rdf
Name: sal
Units: practical salinity units
Description: <p>salinity</p>
http://lod.bco-dmo.org/id/dataset-parameter/471631.rdf
Name: O2
Units: micromoles per kilogram
Description: <p>oxygen</p>
http://lod.bco-dmo.org/id/dataset-parameter/471632.rdf
Name: FITC_2
Units: cells per milliliter
Description: <p>Abundance for eukaryotic microbes retained by a 0.2 mm polycarbonate filter</p>
http://lod.bco-dmo.org/id/dataset-parameter/471633.rdf
Name: FITC_8
Units: cells per milliliter
Description: <p>Abundance (cells ml-1) for eukaryotic microbes retained by a 0.8 mm polycarbonate filter</p>
http://lod.bco-dmo.org/id/dataset-parameter/471634.rdf
Name: EUK516
Units: cells
Description: <p>Relative abundance of cells hybridizing with the universal eukaryote probe EUK516</p>
http://lod.bco-dmo.org/id/dataset-parameter/471635.rdf
Name: KIN516
Units: cells
Description: <p>Relative abundance of cells hybridizing with probe KIN 516 for Kinetoplastida</p>
http://lod.bco-dmo.org/id/dataset-parameter/471636.rdf
Name: LabY
Units: cells
Description: <p>Relative abundance of cells hybridizing with the LabY probe for Labyrinthulomycetes</p>
http://lod.bco-dmo.org/id/dataset-parameter/471637.rdf
Name: PF2
Units: cells
Description: <p>Relative abundance of cells hybridizing with the PF2 probe for fungi</p>
http://lod.bco-dmo.org/id/dataset-parameter/471638.rdf
Name: Alv01
Units: cells
Description: <p>Relative abundance of cells hybridizing with the Alv01 probe for group II Alveolata</p>
http://lod.bco-dmo.org/id/dataset-parameter/471639.rdf
Name: DiploR1792
Units: cells
Description: <p>Relative abundance of cells hybridizing with the DiploR1792 probe for Diplonemids</p>
http://lod.bco-dmo.org/id/dataset-parameter/471640.rdf
Name: NS4
Units: cells
Description: <p>Relative abundance of cells hybridizing with the NS4 probe for type 4 Marine Stramenopiles (MAST 4)</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
29038
https://datadocs.bco-dmo.org/file/rggpGzrUARGJ79/protists.csv
protists.csv
Primary data file for dataset ID 471609
download
https://osprey.bco-dmo.org/dataset/471609/data/download
download
onLine
dataset
<p>Excerpt from Morgan-Smith et al. (2013):</p>
<p>Samples were collected using a rosette sampler fitted with 25 L Niskin bottles. Samples were immediately fixed with 0.2 micron-filtered methanol-stabilized formaldehyde (final concentration ~2%) and kept overnight at room temperature to allow outgassing and prevent bubble formation on filters. Subsamples of 100-250 ml were then filtered under gentle vacuum (-200mbar) onto Millipore 0.2 micron white polycarbonate filters for DAPI-FITC. A pore size of 0.2 micron is preferred for enumeration of total eukaryotes because some smaller eukaryotes are lost through the pores of 0.8 micron filters, leading to underestimation of eukaryote abundance (Morgan-Smith et al., 2011). Filters were washed with phosphate buffered saline (PBS) and ultra-pure water, then immediately stored at -80 C.</p>
<p>DAPI-FITC double staining was used to enumerate total eukaryotes. Pie-shaped slices of approximately 1/16-1/8 of filter were cut and 3-4 of these slices were placed atop a 25 mm diameter, 0.2 micron pore size polycarbonate filter on a glass frit and covered with a 10-ml filter tower, which was then flooded with 1ml FITC staining solution (2.5 ml 0.5 M sodium carbonate buffer, pH 9; 11 ml 0.01 M potassium phosphate buffer, pH 7.2; 11 ml 0.85 % sodium chloride; 10 mg FITC), and incubated for 10 min in the dark. Then vacuum was applied (-200 mbar) and filters were washed twice with 10 ml ice-cold carbonate buffer (0.5M, pH9). Filter sections were mounted on slides using Vectashield mounting medium with DAPI and stored at -20 C until analysis. Samples were counted on Olympus BX51 and BX50 epifluorescence micro scopes.</p>
Specified by the Principal Investigator(s)
<p>Raw counts were converted into cell numbers per ml using field of view under the microscope, filtered area on the polycarbonate filter, and volume filtered as input variables.</p>
<p><strong>References: </strong></p>
<p>Morgan-Smith D., Clouse M. A., Herndl G. J., Bochdansky A. B. (2013) Diversity and distribution of microbial eukaryotes in the deep tropical and subtropical North Atlantic Ocean. Deep-Sea Res. I: 78: 58-69</p>
<p>Morgan-Smith D., Herndl G. J., van Aken H. M., Bochdansky A. B. (2011) Feature article. Abundance of eukaryotic microbes in the deep subtropical North Atlantic. Aquat. Microb. Ecol. 65.</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
Fluorescence Microscope
Fluorescence Microscope
PI Supplied Instrument Name: Fluorescence Microscope PI Supplied Instrument Description:Olympus BX51 and BX50 epifluorescence microscopes Instrument Name: Fluorescence Microscope Instrument Short Name: Instrument Description: Instruments that generate enlarged images of samples using the phenomena of fluorescence and phosphorescence instead of, or in addition to, reflection and absorption of visible light. Includes conventional and inverted instruments. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB06/
Niskin bottle
Niskin bottle
PI Supplied Instrument Name: Niskin bottle PI Supplied Instrument Description:25 liter Niskin bottles Instrument Name: Niskin bottle Instrument Short Name:Niskin bottle Instrument Description: A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/
Cruise: 64PE280
64PE280
R/V Pelagia
Community Standard Description
International Council for the Exploration of the Sea
R/V Pelagia
vessel
64PE280
Dr Gerhard Herndl
Royal Netherlands Institute for Sea Research
http://melia.nioz.nl/phptoweb/dmg/melia-codis.php?script=search/bycruise.inc
Report describing 64PE280
Cruise: 64PE325
64PE325
R/V Pelagia
Community Standard Description
International Council for the Exploration of the Sea
R/V Pelagia
vessel
64PE325
Dr Gerhard Herndl
Universität Wien
http://melia.nioz.nl/phptoweb/dmg/melia-codis.php?script=search/bycruise.inc
Report describing 64PE325
R/V Pelagia
Community Standard Description
International Council for the Exploration of the Sea
R/V Pelagia
vessel