Dataset: MEDEA-II CARD FISH cell counts

Name: 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
Published: 2016-09-16
Keywords: biota, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.658821.1

Spatial Extent: N:67.35 E:-2.69 S:50.86 W:-40.07

Temporal Extent: 2012-06-23 - 2012-07-23

Project:

Ecology of eukaryote microbes in the deep North Atlantic (Eukaryote Microbes NAtl)

Principal Investigator:

Alexander B. Bochdansky (Old Dominion University, ODU)

BCO-DMO Data Manager:

Nancy Copley (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2016-09-16

Restricted:

Validated:

Yes

Current State:

Final no updates expected

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

Abstract:

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.

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2016-09-16	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.658821.1	2021-02-25

Methods & Sampling

For methodology, see Bochdansky, A. B., M. A. Clouse, G. J. Herndl (2016). (exerpt: PDF)
For Medea 2 Oligonucleotide probe sequences and evaluation details, see Supplemental Files. (PDF)

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)).

Data Processing Description

BCO-DMO Processing:
- added conventional header with dataset name, PI name, version date, reference information
- renamed parameters to BCO-DMO standard
- transformed Word doc table to flat files
- added lat and lon columns

Data Files

File
CARD_FISH_30um_filter.csv (Comma Separated Values (.csv), 3.28 KB) MD5:68f3362ec738fae4340a46eea9ae5888 Primary data file for dataset ID 658821

Supplemental Files

File
Medea 2 Oligonucleotide probe sequences and evaluation details filename: MEDEA_II_cardfish_Oligonucleotide_probe_sequences_eval.pdf (Portable Document Format (.pdf), 155.38 KB) MD5:17521da3260bebaf8c8f2c387695ea1d

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1235169

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
64PE356	MEDEA II Medea 2	2012-06-23	R/V Pelagia	Dr Gerhard Herndl (Chief Scientist)	data info

Instruments

Fluorescence Microscope

Supplied Name:

Supplied Description:

Olympus BX51 epifluorescence microscope, U-LH100HG APO mercury burner, 100 x UPlanSApo objective lens, and 20 x ocular magnification.

Instrument Type

Generic Name: Fluorescence Microscope

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB06/

Generic 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.

Niskin bottle

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Niskin bottle

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/

Generic 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.

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
filter_name	Sample label (filter name) indicating the station and pore size of filter	unitless	sample
station	Station number	unitless	sta
lat	Latitude; north is positive	decimal degrees	lat
lon	Longitude; east is positive	decimal degrees	lon
pore_size	Filter pore size	micrometers (um)	filter_size
EKD_NEN	Normalized eukaryote numbers (NEN); number of eukaryotes counted using the EKD probes combined divided by the number of prokaryotes counted using DAPI counter stain	ratio	count
EKD_RER	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	ratio	no_bcodmo_term
Kin_NEN	Normalized eukaryote numbers (NEN); number of kinetoplastids counted using the KIN516 probe divided by the number of prokaryotes counted using DAPI counter stain	ratio	count
Kin_RER	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	ratio	no_bcodmo_term
LabY_NEN	Normalized eukaryote numbers (NEN); number of labyrithulomycetes counted using the LabY probe divided by the number of prokaryotes counted using DAPI counter stain	ratio	count
LabY_RER	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	ratio	no_bcodmo_term
PF2_NEN	Normalized eukaryote numbers (NEN); number of fungi counted using the PF2 probe divided by the number of prokaryotes counted using DAPI counter stain	ratio	count
PF2_RER	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	ratio	no_bcodmo_term

Status message

Database

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Dataset: MEDEA-II CARD FISH cell counts