Dataset: EN638 Bulk Cell Counts

Name: Bulk water cell abundance of samples taken aboard the R/V Endeavor EN638, May 2019 in the Northern Atlantic
Published: 2020-08-14
Keywords: carbon cycling, cell abundance, Northwest Atlantic, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.820961.1

Spatial Extent: N:42.83954 E:-53.3949 S:34.50102 W:-75.67819

Temporal Extent: 2019-05-15 - 2019-05-25

Project:

A mechanistic microbial underpinning for the size-reactivity continuum of dissolved organic carbon degradation (Microbial DOC Degradation)

Principal Investigator:

Carol Arnosti (University of North Carolina at Chapel Hill, UNC-Chapel Hill)

Contact:

Carol Arnosti (University of North Carolina at Chapel Hill, UNC-Chapel Hill)

BCO-DMO Data Manager:

Karen Soenen (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2020-08-14

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Bulk water cell abundance of samples taken aboard the R/V Endeavor EN638, May 2019 in the Northern Atlantic

Abstract:

Bulk water cell abundance of samples taken aboard the R/V Endeavor EN638, May 2019 in the Northern Atlantic

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2020-08-14	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.820961.1	2020-09-24

Description

Measurements of bulk water cell abundance from RV/Endeavor EN638, May 2019 in the Northern Atlantic.

Methods & Sampling

For each depth, 20-30 ml of 1% formaldehyde (FA) fixed sample were filtered through a 0.2 µm pore size poly-carbonate filter, applying a maximum vacuum of 200 mbar. Nucleic acids of filtered cells were counterstained with 4',6-diamidino-2-phenylindole (DAPI) and mounted using a Citifluor/VectaShield (4:1) solution. Cell abundance was measured on a fully automated epifluorescence microscope as described by Bennke et al., 2016, with a minimum of 45 fields of view (FOV) per sample were acquired using a 63x magnification oil immersion plan apochromatic objective with a numerical aperture of 1.4 (Carl Zeiss). Validation of the automated counts was done by manual cell counting.

Data Processing Description

Cell counting was performed with a fully automated epifluorescence microscope as described by Bennke et al., 2016 and image analysis software ACMETOOL (http://www.technobiology.ch and Max Planck Institute for marine microbiology, Bremen). Excel

BCO-DMO processing note:

Adjusted column names to comply with database requirements
Added ISO_DateTine_UTC column
Converted data to ISO format (yyyy-mm-dd)

Data Files

File
bulk_cell_counts.csv (Comma Separated Values (.csv), 2.37 KB) MD5:336aa14fb763159d231a37d950edaa79 Primary data file for dataset ID 820961

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1736772

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
EN638		2019-05-15	R/V Endeavor	Carol Arnosti (Chief Scientist)	data info

Instruments

Camera

Supplied Name: Cooled charged-coupled-device camera (AxioCam MRm )

Supplied Description:

An automated epifluorescence microscope (Zeiss AxioImager.Z2 microscope stand, Carl Zeiss Jena, Gemany) equipped with a cooled charged-coupled-device (CCD) camera (AxioCam MRm + Colibri LED light source, Carl Zeiss), a light-emitting diode for DAPI (UV-emitting LED, 365 nm) and a HE-62 multi filter module with a triple emission filter (425/50 nm, 527/54 nm, LP 615 nm, including a triple beam splitter of 395/495/610, Carl Zeiss).

Instrument Type

Generic Name: Camera

Acronym: camera

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/311/

Generic Description:

All types of photographic equipment including stills, video, film and digital systems.

Fluorescence Microscope

Supplied Name: Zeiss Axio Imager Epifluorescence microscope

Supplied Description:

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.

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
deployment	Cruise ID	unitless	cruise_id
station	Station number for cruise	unitless	station
longitude	Longitude, south is negative	decimal degrees	lon
latitude	Latitude, west is negative	decimal degrees	lat
date	Date of sample collection in ISO format (yyyy-mm-dd), US Eastern Time (UTC-05:00)	unitless	date
time	Time of sample collection in ISO format (hh:mm:ss), US Eastern Time (UTC-05:00)	unitless	time
cast_number	Cast number (refers to cast of CTD/Niskin bottles on cruise)	unitless	cast
depth_sequence	Sequence of depths sampled (1 is surface; higher numbers at greater depths)	unitless	depth
depth_actual	Actual depth at which water was collected	meters (m)	depth
sample_type	Sample from bulk water or Large Volume incubation	unitless	sample_descrip
unammended_ammended	Whether high molecular weight thalassiosira weissflogii extract was added or not; A, B, C refers to incubation depth, and the following number corresponds to incubation replicate.	unitless	sample_descrip
cell_count	Number of cells per mL	cells per mL	count
ISO_DateTime_UTC	Datetime of sample collection in ISO format in UTC timezone (yyyy-mm-dd:hh:mm:ssZ)	yyyy-MM-dd'T'HH:mm:ss'Z'	ISO_DateTime_UTC

Status message

Database

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Dataset: EN638 Bulk Cell Counts