Dataset: Coastal SAR11 Physiochemical data
Deployment: Coastal_SAR11

Physiochemical data from samples collected along the coast of Louisiana, USA during 2018.

Principal Investigator:

J. Cameron Thrash (University of Southern California, USC)

Co-Principal Investigator:

Elizabeth Kujawinski (Woods Hole Oceanographic Institution, WHOI)

Contact:

J. Cameron Thrash (University of Southern California, USC)

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

Collaborative Research: EAGER: Salinity-based selection between sister clades of abundant coastal bacterioplankton (CoastalSAR11)

Current State:

Final no updates expected

Version:

Data URL:

https://www.bco-dmo.org/dataset-deployment/745481/data

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Description

Physiochemical data from samples collected along the coast of Louisiana in the Gulf of Mexico.

Methods & Sampling

Dataset acquisition description

Samples were collected manually by filling an acid-washed and autoclaved 20L carboy after three rinses. Temperature, pH, and salinity were taken using a handheld YSI. Cell counts were obtained by filtering water through a 2.7 µm Whatman GF/D filter, fixing with 10% formaldehyde, placing on ice, and then counting using flow cytometry (Thrash et al., 2015, Hydrocarbon and Lipid Microbiology Protocols). Inorganic nutrients were measured at the University of Washington Marine Chemistry Laboratory after sequential filtration through 2.7 Whatman GF/D and 0.22 µm Sterivex filters. Samples were initially placed on ice in the field, and then refrigerated until shipment with ice packs.

Data Processing Description

Dataset Processing Description

Data Problem Report:
pH is not reported for the first time points because a crack was noticed in the housing of the YSI cable that seemed to be associated with calibration. This was subsequently replaced and all values were also checked in the lab with a Fisherbrand pH meter.

Sample ARD 9/19/18 was not filtered on site because of bad weather. Therefore, the filtration steps for nutrients were conducted back at the lab after a 2.5 hour transit time

Sample ARD 11/16/18 was filtered for nutrients after a 3 hour delay at site CJ because of power supply issues at the ARD site.

BCO-DMO Data Processing Notes:
-Reformatted column names to comply with BCO-DMO standards;
-Replaced blank cells with nd;
-Reformatted dates;
-Added ISO DateTime column.

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1747681	NSF Division of Ocean Sciences
OCE-1747722	NSF Division of Ocean Sciences
OCE-1931113	NSF Division of Ocean Sciences

Instruments

Flow Cytometer

Supplied Name: Millipore Guava 5HT HPL benchtop flow cytometer

Supplied Description:

Used for sampling

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)

Multi Parameter Portable Meter

Supplied Name: YSI 556 MPS handheld meter

Supplied Description:

YSI 556 MPS handheld meter, calibrated with salinity and pH standards immediately prior to use

Instrument Type

Generic Name: Multi Parameter Portable Meter

Generic Description:

An analytical instrument that can measure multiple parameters, such as pH, EC, TDS, DO and temperature with one device and is portable or hand-held.

Pump

Supplied Name: Masterflex I/P peristaltic pump

Supplied Description:

Used for sampling

Instrument Type

Generic Name: Pump

Generic Description:

A pump is a device that moves fluids (liquids or gases), or sometimes slurries, by mechanical action. Pumps can be classified into three major groups according to the method they use to move the fluid: direct lift, displacement, and gravity pumps

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
Site	Sampling site designation	unitless	site
Lat	Latitude of site	decimal degrees	lat
Lon	Longitude of site	decimal degrees	lon
Date	Date of sampling; format: yyyy-mm-dd	unitless	date
Time_Central	Time of sampling in the Central Time Zone, USA; format: HH:MM	unitless	time
Offset	Universal time coordinated (UTC) offset, corrected for daylight savings	unitless	time_diff
Time_UTC	Universal Time Coordinated (UTC) subtracting Central Time from the UTC offset; format: HH:MM	unitless	time
Temp	Temperature measured via YSI at the sampling site	degrees Celsius	temperature
Cond	Conductivity measured via YSI at the sampling site	ms/cm	cond
Salinity	Calculated salinity based on the conductivity measurement from the YSI	unitless	sal
pH	pH of the seawater at the sampling site	unitless	pH
Cell_counts	Number of cells passing through a 2.7 µm filter (Whatman GF/D) determined via flow cytometry	cells/mL	count
PO4	Concentration of phosphate in seawater from the site	umol/L	PO4
SiOH4	Concentration of silicate in seawater from the site	umol/L	Silicate
NO3	Concentration of nitrate in seawater from the site	umol/L	NO3
NO2	Concentration of nitrite in seawater from the site	umol/L	NO2
NH4	Concentration of ammonium in seawater from the site	umol/L	NH4
ISO_DateTime_UTC	Date and time of sampling (UTC) formatted to ISO 8601 standard; format: yyyy-mm-ddTHH:MMZ	unitless	ISO_DateTime_UTC

Database

Contribute Data

Dataset: Coastal SAR11 Physiochemical data
Deployment: Coastal_SAR11

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Coastal SAR11 Physiochemical dataDeployment: Coastal_SAR11

Dataset acquisition description

Dataset Processing Description

Dataset: Coastal SAR11 Physiochemical data
Deployment: Coastal_SAR11