Dataset: Bacteria Counts CTD Bottle Measurements
Deployment: HRS2204

Bacteria Counts CTD Bottle Measurements HRS2204

View Data: For data, See Dataset Metadata Page: https://osprey.bco-dmo.org/dataset/945987

Principal Investigator:

Matthew Rau (Pennsylvania State University, PSU)

Scientist:

Kimberlee Thamatrakoln (Rutgers University)

Student:

Austin Grubb (Rutgers University)

BCO-DMO Data Manager:

Audrey Mickle (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

Collaborative Research: The importance of particle disaggregation on biogeochemical flux predictions (Disaggregation)

Version:

Deployment Synonyms:

GoM22 cruise

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Description

Methods & Sampling

Dataset acquisition description

This cruise visited eight stations on the Northeastern U.S. Continental Shelf. Latitudes and longitudes provided per sample in the data, but general station descriptions are below.

Station 1 - Station 3: Georges Bank near the Gulf of Maine. Approximate location was 41.7 N, 68 W. Samples acquired from 0 m to 25 m depths.
Station 4: The Great South Channel near the Gulf of Maine. Approximate location was 41.6 N, 69 W. Samples acquired from 0 m to 150 m depths.
Station 5: Only one CTD profile was taken before this station was aborted due to weather. No data acquired. Station location was 40.8 N, 70.5 W.
Station 6: Off the coast of Martha's Vineyard. Approximate location was 41.3 N, 70.5 W. Samples acquired from 0 m to 10 m depths.
Station 7: At the mouth of the Sakonnet River near Newport, Rhode Island. Approximate location was 41.5 N, 71.2 W. Samples acquired from 0 m to 10 m depths.
Station 8: Hudson Canyon near New York. Approximate location was 39.5 N, 72.3 W. Samples acquired from 0 m to 200 m depths.

Whole seawater and 1.2 um filtrates were fixed in final concentration of 0.5% glutaraldehyde for 15 min at 4 degrees, then flash frozen in liquid N2 and stored at -20 degree until analysis. Samples were thawed at room temperature and 10 ug/ml Tween-80 (final concentration) was added to each. Samples were sonicated for 1 min in a water bath (50W). A 20,000-fold dilution of Sybr Green I Nucleic Acid stain (Thermo-Fisher) was made in 0.2 um filtered 1XTE. 5ul of sample was mixed with 245 ul of 1X TE/Sybr Green I in a 96 well microtiter plate. Samples were counted on an Accrui C6 Plus flow cytometer on a fast flow rate, triggered off FL1-H<1000 for 30 sec.

Data Processing Description

Dataset Processing Description

Particle associated bacteria were calculated by subtracting concentrations of the 1.2 micron filtrate from the concentrations obtained for whole seawater. Free and particle-associated bacteria concentrations were calculated from raw counts accounting for dilutions. Other data processing was not applicable.

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1948283	NSF Division of Ocean Sciences

Instruments

CTD Sea-Bird 911

Supplied Name: CTD

Supplied Description:

These data include measurements of free bacteria in whole seawater and particle-associated bacteria for particles larger than 1.2 microns from CTD bottle water samples collected during a cruise on the Northeast Continental Shelf to study particle disaggregation.

Instrument Type

Generic Name: CTD Sea-Bird 911

Acronym: CTD SBE 911

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0035/

Generic Description:

The Sea-Bird SBE 911 is a type of CTD instrument package. The SBE 911 includes the SBE 9 Underwater Unit and the SBE 11 Deck Unit (for real-time readout using conductive wire) for deployment from a vessel. The combination of the SBE 9 and SBE 11 is called a SBE 911. The SBE 9 uses Sea-Bird's standard modular temperature and conductivity sensors (SBE 3 and SBE 4). The SBE 9 CTD can be configured with auxiliary sensors to measure other parameters including dissolved oxygen, pH, turbidity, fluorescence, light (PAR), light transmission, etc.). More information from Sea-Bird Electronics.

Flow Cytometer

Supplied Name: Accrui C6 Plus flow cytometer

Supplied Description:

Samples were counted on an Accrui C6 Plus flow cytometer.

Instrument Type

Generic Name: Flow Cytometer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB37/

Generic Description:

Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells.
(from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm)

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
ID	ID of the CTD cast sample, formatted as (station#_CTDcast#_depth)	unitless	bottle
Station	Station number	unitless	station
CTD	CTD cast number	unitless	cast
Depth	Depth in meters that the CTD bottle was triggered for sampling	meters (m)	depth
ISO_DateTime_UTC	ISO datetime the sample was acquired in UTC	unitless	ISO_DateTime_UTC
Date_UTC	UTC date on which the sample was acquired	unitless	date
Time_UTC	UTC time when the sample was acquired	unitless	time
Latitude	Ship's latitude when the sample was taken	decimal degrees	lat
Longitude	Ship's longitude when the sample was taken	decimal degrees	lon
Free_bacteria	Bacteria concentration in 1.2 micron filtered fraction	cells/ml	bact_abund
Bacteria_concentration_diff	Bacteria concentration of whole seawater minus that in 1.2 micron filtered fraction	cells/ml	bact_abund

Database

Contribute Data

Dataset: Bacteria Counts CTD Bottle Measurements
Deployment: HRS2204

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Bacteria Counts CTD Bottle MeasurementsDeployment: HRS2204

Dataset acquisition description

Dataset Processing Description

Dataset: Bacteria Counts CTD Bottle Measurements
Deployment: HRS2204