http://lod.bco-dmo.org/id/dataset/658821
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
2016-09-16
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
CARD FISH Eukaryote, Fungi, Labyrinthomycete, Kinetoplastid counts from MEDEA-II R/V Pelagia 64PE356 in the North Atlantic: Galway, Ireland to Reykjavik, Iceland from June to July 2012
2016-09-16
publication
2016-09-16
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-02-25
publication
https://doi.org/10.26008/1912/bco-dmo.658821.1
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. (2021) CARD FISH Eukaryote, Fungi, Labyrinthomycete, Kinetoplastid counts from MEDEA-II R/V Pelagia 64PE356 in the North Atlantic: Galway, Ireland to Reykjavik, Iceland from June to July 2012. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2016-09-16 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.658821.1 [access date]
MEDEA-II stations for CARD FISH samples Dataset Description: Methods and Sampling: <p>For methodology, see Bochdansky, A. B., M. A. Clouse, G. J. Herndl (2016).&nbsp;(exerpt:&nbsp;<a href="http://dmoserv3.bco-dmo.org/data_docs/Eukaryote_Microbes_NAtl/MEDEA_II_cardfish_methods.pdf" target="_blank">PDF</a>)<br />
For Medea 2 Oligonucleotide probe sequences and evaluation details, see Supplemental Files.&nbsp;(<a href="http://dmoserv3.bco-dmo.org/data_docs/Eukaryote_Microbes_NAtl/MEDEA_II_cardfish_Oligonucleotide_probe_sequences_eval.pdf" target="_blank">PDF</a>)</p>
<p>Raw lengths were converted into micrometers using a calibration curve with relative object distance. The calibration equation is =uncorrected length/(1+0.00893*(object distance/1000)).</p>
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
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
Dataset Version: 1
Unknown
filter_name
station
lat
lon
pore_size
EKD_NEN
EKD_RER
Kin_NEN
Kin_RER
LabY_NEN
LabY_RER
PF2_NEN
PF2_RER
theme
None, User defined
sample identification
station number
latitude
longitude
filter_size
count
No BCO-DMO term
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
-40.07
-2.69
50.86
67.35
2012-06-23
2012-07-23
Temparate, subarctic Atlantic and Arctic Ocean
0
BCO-DMO catalogue of parameters from CARD FISH Eukaryote, Fungi, Labyrinthomycete, Kinetoplastid counts from MEDEA-II R/V Pelagia 64PE356 in the North Atlantic: Galway, Ireland to Reykjavik, Iceland from June to July 2012
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/658842.rdf
Name: filter_name
Units: unitless
Description: <p>Sample label (filter name) indicating the station and pore size of filter</p>
http://lod.bco-dmo.org/id/dataset-parameter/658843.rdf
Name: station
Units: unitless
Description: <p>Station number</p>
http://lod.bco-dmo.org/id/dataset-parameter/658844.rdf
Name: lat
Units: decimal degrees
Description: <p>Latitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/658845.rdf
Name: lon
Units: decimal degrees
Description: <p>Longitude; east is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/658846.rdf
Name: pore_size
Units: micrometers (um)
Description: <p>Filter pore size</p>
http://lod.bco-dmo.org/id/dataset-parameter/658847.rdf
Name: EKD_NEN
Units: ratio
Description: <p>Normalized eukaryote numbers (NEN); number of eukaryotes counted using the EKD probes combined divided by the number of prokaryotes counted using DAPI counter stain</p>
http://lod.bco-dmo.org/id/dataset-parameter/658848.rdf
Name: EKD_RER
Units: ratio
Description: <p>Relative enrichment ratios (RER) of eukaryotes over prokaryotes on the 30 micrometer pore-size filters versus 0.2 micrometer pore-size filters; mathematically: NEN on the 30 micron filter divided by the NEN on the 0.2 micron filters for all eukaryotes</p>
http://lod.bco-dmo.org/id/dataset-parameter/658849.rdf
Name: Kin_NEN
Units: ratio
Description: <p>Normalized eukaryote numbers (NEN); number of kinetoplastids counted using the KIN516 probe divided by the number of prokaryotes counted using DAPI counter stain</p>
http://lod.bco-dmo.org/id/dataset-parameter/658850.rdf
Name: Kin_RER
Units: ratio
Description: <p>Relative enrichment ratios (RER) of kinetoplastids over prokaryotes on the 30 micrometer pore-size filters versus 0.2 micrometer pore-size filters; mathematically: NEN on the 30 micron filter divided by the NEN on the 0.2 micron filters for kinetoplastids</p>
http://lod.bco-dmo.org/id/dataset-parameter/658851.rdf
Name: LabY_NEN
Units: ratio
Description: <p>Normalized eukaryote numbers (NEN); number of labyrithulomycetes counted using the LabY probe divided by the number of prokaryotes counted using DAPI counter stain</p>
http://lod.bco-dmo.org/id/dataset-parameter/658852.rdf
Name: LabY_RER
Units: ratio
Description: <p>Relative enrichment ratios (RER) of labyrithulomycetes over prokaryotes on the 30 micrometer pore-size filters versus 0.2 micrometer pore-size filters; mathematically: NEN on the 30 micron filter divided by the NEN on the 0.2 micron filters for labyrithulomycetes</p>
http://lod.bco-dmo.org/id/dataset-parameter/658853.rdf
Name: PF2_NEN
Units: ratio
Description: <p>Normalized eukaryote numbers (NEN); number of fungi counted using the PF2 probe divided by the number of prokaryotes counted using DAPI counter stain</p>
http://lod.bco-dmo.org/id/dataset-parameter/658854.rdf
Name: PF2_RER
Units: ratio
Description: <p>Relative enrichment ratios (RER) of fungi over prokaryotes on the 30 micrometer pore-size filters versus 0.2 micrometer pore-size filters; mathematically: NEN on the 30 micron filter divided by the NEN on the 0.2 micron filters for fungi</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
3361
https://darchive.mblwhoilibrary.org/bitstream/1912/26743/1/dataset-658821_medea-ii-card-fish-cell-counts__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.658821.1
download
onLine
dataset
<p>For methodology, see Bochdansky, A. B., M. A. Clouse, G. J. Herndl (2016).&nbsp;(exerpt:&nbsp;<a href="http://dmoserv3.bco-dmo.org/data_docs/Eukaryote_Microbes_NAtl/MEDEA_II_cardfish_methods.pdf" target="_blank">PDF</a>)<br />
For Medea 2 Oligonucleotide probe sequences and evaluation details, see Supplemental Files.&nbsp;(<a href="http://dmoserv3.bco-dmo.org/data_docs/Eukaryote_Microbes_NAtl/MEDEA_II_cardfish_Oligonucleotide_probe_sequences_eval.pdf" target="_blank">PDF</a>)</p>
<p>Raw lengths were converted into micrometers using a calibration curve with relative object distance. The calibration equation is =uncorrected length/(1+0.00893*(object distance/1000)).</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing:</strong><br />
- added conventional header with dataset name, PI name, version date, reference information<br />
- renamed parameters to BCO-DMO standard<br />
- transformed Word doc table&nbsp;to flat files<br />
- added lat and lon columns</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:Olympus BX51 epifluorescence microscope, U-LH100HG APO mercury burner, 100 x UPlanSApo objective lens, and 20 x ocular magnification. 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/
PI Supplied Instrument Name: 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