Dataset: Bacteria Counts CTD Bottle Measurements

Name: Bacteria Counts CTD Bottle Measurements from CTD samples collected during R/V Hugh R. Sharp cruise HRS2204 from Apr to May 2022
Published: 2024-12-16
Keywords: bacteria, particle-attached bacteria, biota, oceans

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Spatial Extent: N:41.7749 E:-67.3996 S:39.4554 W:-72.2765

Northeastern U.S. Continental Shelf

Temporal Extent: 2023-04-23 - 2024-05-01

Project:

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

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)

Version:

Version Date:

2024-12-16

Restricted:

Validated:

Current State:

Preliminary and in progress

Bacteria Counts CTD Bottle Measurements from CTD samples collected during R/V Hugh R. Sharp cruise HRS2204 from Apr to May 2022

Abstract:

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. One cruise was completed aboard the R/V Hugh R. Sharp from 2022-04-21 through 2022-05-02 (HRS 22-04), which visited a variety of stations and hydrodynamic environments associated with the Northeast Continental Shelf of the United States. Stations ranged from Georges Bank and the Great South Channel near the Gulf of Maine, Martha's Vineyard, the mouth of the Sakonnet River near Newport, Rhode Island, and Hudson Canyon near New York. These data were collected as part of a study to clarify the importance of hydrodynamic forces on the cohesion, aggregation, and breakup of marine particles. These data were collected by Dr. Austin Grubb of the Rutgers University on the cruise led by Dr. Matthew Rau (chief-sci) of the George Washington University.

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Methods & Sampling

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.

Problems/Issues

The particle-associated bacteria counts at some stations/depths were quite low, resulting in negative values after subtracting as described in the data processing above.

Data 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.

BCO-DMO Processing

- Imported "HRS22-04_BacteriaCounts.xlsx" into the BCO-DMO system
- Combined date and times to create datetime field
- Renamed fields to comply with BCO-DMO naming conventions
- Exported final file as "945987_v1_bacteria_counts_ctd.csv"

More Information about this dataset

Funding Sources

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

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
HRS2204	GoM22 cruise	2022-04-21	R/V Hugh R. Sharp	Matthew Rau (Chief Scientist)	data info

Instruments

CTD Sea-Bird 911

Supplied Name: CTD

Supplied Description:

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

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

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 Format: %Y-%m-%dT%H:%M:%SZ	unitless	ISO_DateTime_UTC
Date_UTC	UTC date on which the sample was acquired Format: %d-%b-%y	unitless	date
Time_UTC	UTC time when the sample was acquired Format: %H:%M:%S	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

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Dataset: Bacteria Counts CTD Bottle Measurements