http://lod.bco-dmo.org/id/dataset/565129
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
2015-08-31
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Protist numbers in subtropical North Atlantic at and below 100 m collected on the R/V Pelagia (64PE356) from Galway, Ireland to Reykjavik, Iceland in 2010 (Eukaryote Microbes NAtl project)
2015-08-31
publication
2015-08-31
revision
BCO-DMO Linked Data URI
2015-08-31
creation
http://lod.bco-dmo.org/id/dataset/565129
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. (2015) Protist numbers in subtropical North Atlantic at and below 100 m collected on the R/V Pelagia (64PE356) from Galway, Ireland to Reykjavik, Iceland in 2010 (Eukaryote Microbes NAtl project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2015-08-31) Version Date 2015-08-31 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/565129 [access date]
Protist numbers in subtropical North Atlantic at and below 100 m Dataset Description: <p>Excerpt from Bochdansky et al. (submitted):</p>
<p>"The Medea-2 expedition on the RV Pelagia (Royal Netherlands Institute for Sea Research) took place from mid June to mid July 2012. Twenty-four stations were sampled from the Porcupine Plains west towards the Charlie-Gibbs Fracture Zone, and then north to the Norwegian Sea. Water from six depths (ranging from 100 - 4483 m), four below 1000 m, one at the oxygen minimum zone (OMZ), and one at 100 m, was collected from 25 L Niskin bottles into 250 mL polycarbonate bottles. Various volumes of water were filtered onto 0.2 µm pore size, 25 mm diameter polycarbonate filters depending on depth: 50 mL from 100 m, 150 mL from the OMZ, and 250 mL from the deep sea and fixed the same way as stated above.&nbsp; The filters were stored in 2 mL cryovials at -80 °C immediately after filtering and shipped to Old Dominion University on dry ice. The filters were cut into 8ths.&nbsp; For prokaryote abundance, two opposite slices were stained and mounted with Vectashield DAPIon glass slides. For eukaryotic microbe abundance, two opposite filter slices were dual-stained with FITC and Vectashield DAPI, and enumerated (Morgan-Smith et al. 2011). All prokaryote and eukaryotic microbe counts were performed on an epifluorescence microscope (Olympus BX51). For prokaryotes a minimum of 50 randomly selected fields of view, 25 on each filter slice, were counted. For eukaryotic microbes, a minimum of 100 randomly selected fields of view was counted per station, 50 from each filter slice."</p>
<p>Cell counts of eukaryotic microbes can be found in &nbsp;the&nbsp;<a href="http://www.bco-dmo.org/dataset-deployment/471615" target="_blank">Protist counts for the cruise Archimedes-IV&nbsp;dataset</a><strong>.</strong> Context data for this cruise are stored on the Centralized Oceanographic Data Information System (CODIS) of the Data Management Group at the Netherlands Institute of Sea Research (<a href="http://www.nioz.nl/portals-en" target="_blank">www.nioz.nl/portals-en</a>). Cruise number: <strong>64PE356</strong>. (not yet available,&nbsp;2015-09-01)</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. doi:10.1016/j.dsr.2013.04.010</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. 65:103-115. doi: 10.3354/ame01536</p>
<p><strong>Related datasets:</strong>&nbsp;See Dataset Collections&nbsp;under the project page for "<a href="http://www.bco-dmo.org/project/2290" target="_blank">Basin-scale distribution and activity of deep-sea protists in the North Atlantic Ocean</a>"</p> Methods and Sampling:
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1235169 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1235169
onGoing
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
Dataset Version: 2015-08-31
Unknown
cruise_id
sta
lat
lon
depth_w
depth
temp
Prokaryotes
Eukaryotes
Niskin bottle
theme
None, User defined
Cruise identfier
station number
latitude
longitude
depth_w
depth
water temperature at measurement depth
abundance
featureType
BCO-DMO Standard Parameters
Fluorescence Microscope
Niskin bottle
instrument
BCO-DMO Standard Instruments
64PE356
service
Deployment Activity
North Atlantic: Galway, Ireland to Reykjavik, Iceland
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.
Ecology of eukaryote microbes in the deep North Atlantic
https://osprey.bco-dmo.org/project/564660
Ecology of eukaryote microbes in the deep North Atlantic
<p><em>Description from NSF award abstract:</em><br />
In the microbial realm, one of the three domains of life -- the Eukarya -- has received little attention in deep-sea research. This stands in contrast to the fact that in all known aquatic environments, and measured by the amount of material and energy transferred, the link between prokaryotic and eukaryotic cells is one of the most significant trophic interactions on Earth. In terms of volume, the deep sea is the largest biome, and despite its tremendous role in long-term biogeochemical cycles, it has largely been neglected. Biological activity in the deep sea is neither negligible nor homogeneous in space and time. Recent data suggest that biological activity in the dark ocean (as evidenced by respiration rates, bacterial secondary production and a variety of other metrics) is much higher than anticipated from all known organic carbon fuel sources combined (i.e., POC flux, DOC convection, in situ production and active transport by zooplankton). Water masses in the deep ocean represent highly-diverse biogeographic regions with distinct communities and particle distributions. Moreover, because of feeding thresholds, cold temperatures, extreme pressures and unique adaptations that deep-sea microbes exhibit, biological activity rules cannot simply be extrapolated from laboratory cultures and from experiments with surface-dwelling microbes. This study focuses on the fundamental role of eukaryotic microbial communities in deep-sea ecology with the overarching hypothesis that protists represent sensitive biological indicators of utilizable organic carbon. There is good reason to believe that microbial eukaryotes and their activities are better indicators of "new" sources of organic carbon than particle inventories, sediment traps, isotope ratios, or models based on surface production and theoretical flux attenuation. For these new biological indicators to work, however, one needs to separate live from the moribund and dead cells, the bacterivores from saprotrophs, the inactive resting stages from those actively feeding on prokaryotes, the gametes and zoospores from vegetative and feeding stages, and those located on particles from the ones freely suspended in the water column. Each of these groups represents different levels of per-cell energy and carbon requirements.</p>
<p>This study determines the ecological role of eukaryotic microbes in the deep North Atlantic over large geographic regions. The research incorporates two fundamentally different experimental designs that capitalize on different time scales: 1) Short-term incubations (~72 hours) of respiratory activity and bacterivory combined with a high resolution sampling of abundances across large geographic regions performed from a research vessel, and 2) Long-term incubations (=/> 4 weeks) measuring colonization of sinking particles and growth of eukaryotic microbes using free-falling (untethered) vehicles representing the first attempt of physiological rate measurements directly in the deep sea. Methods include new tracers for bacterivory, incubations for single-cell respiration, taxonomic identification using fluorescence in situ hybridization, single-cell genomics, and the first of its kind deep-sea holographic microscope capturing images to a maximum depth of 6000 m at 5 micrometer resolution.</p>
Eukaryote Microbes NAtl
largerWorkCitation
project
eng; USA
biota
oceans
North Atlantic: Galway, Ireland to Reykjavik, Iceland
2015-08-31
Temparate, subarctic Atlantic and Arctic Ocean
0
BCO-DMO catalogue of parameters from Protist numbers in subtropical North Atlantic at and below 100 m collected on the R/V Pelagia (64PE356) from Galway, Ireland to Reykjavik, Iceland in 2010 (Eukaryote Microbes NAtl 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/565165.rdf
Name: cruise_id
Units: unitless
Description: <p>cruise identification</p>
http://lod.bco-dmo.org/id/dataset-parameter/565166.rdf
Name: sta
Units: unitless
Description: <p>station number</p>
http://lod.bco-dmo.org/id/dataset-parameter/565167.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/565168.rdf
Name: lon
Units: decimal degrees
Description: <p>longitude; east is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/565169.rdf
Name: depth_w
Units: meters
Description: <p>depth of the water</p>
http://lod.bco-dmo.org/id/dataset-parameter/565170.rdf
Name: depth
Units: meters
Description: <p>sample depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/565171.rdf
Name: temp
Units: degrees Celsius
Description: <p>temperature</p>
http://lod.bco-dmo.org/id/dataset-parameter/565172.rdf
Name: Prokaryotes
Units: cells/ml
Description: <p>prokaryote cell numbers (Bacteria + Archaea)</p>
http://lod.bco-dmo.org/id/dataset-parameter/565173.rdf
Name: Eukaryotes
Units: cells/ml
Description: <p>Protist cell numbers (eukaryotic microbes)</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
12818
https://datadocs.bco-dmo.org/file/zqqA8RRFG1GvLk/protists_prokaryotes_MEDEAII.csv
protists_prokaryotes_MEDEAII.csv
Primary data file for dataset ID 565129
download
https://osprey.bco-dmo.org/dataset/565129/data/download
download
onLine
dataset
<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>BCO-DMO Processing:</strong></p>
<p>- added conventional header with dataset name, PI name, version date<br />
- renamed parameters to BCO-DMO standard<br />
- replaced blank cells with nd's (no data)<br />
- id column not served<br />
- converted 360 lons to 180 lons</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
PI Supplied Instrument Name: PI Supplied Instrument Description:Epifluorescence microscope (Olympus BX51) 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 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: 64PE356
64PE356
R/V Pelagia
Community Standard Description
International Council for the Exploration of the Sea
R/V Pelagia
vessel
64PE356
Dr Gerhard Herndl
Universität Wien
R/V Pelagia
Community Standard Description
International Council for the Exploration of the Sea
R/V Pelagia
vessel