Dataset: Bacterial Growth ACTivity

Name: Bacterial and viral cell counts, and nutrients from 5 cruises on the R/V Hugh R. Sharp in Delaware and Chesapeake Bays, 2014-2016 (Coastal Bacterial Growth Rates project)
Published: 2016-03-31
Keywords: biota, oceans

Cite This Dataset

Spatial Extent: N:39.8708 E:-74.9167 S:36.97 W:-76.6478

Project:

Growth Rates of Bacterial Taxa in Coastal Marine Ecosystems (Coastal Bacterial Growth Rates)

Principal Investigator:

Dr Barbara Campbell (Clemson University, Clemson)

BCO-DMO Data Manager:

Ms Dicky Allison (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

waiting for validation

Version Date:

2016-03-31

Restricted:

Validated:

Current State:

Final no updates expected

Bacterial and viral cell counts, and nutrients from 5 cruises on the R/V Hugh R. Sharp in Delaware and Chesapeake Bays, 2014-2016 (Coastal Bacterial Growth Rates project)

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Description

Standard oceanographic measurements collected from CTD casts during 5 cruises in Delaware and Chesapeake Bays, representing coastal marine ecosystems. Measurements included nutrients, chlorophyll and light attenuation, bacterial and viral production.

This is a new version with both new data and updated older data. March 31, 2016

DMO notes:

changed ND to nd
,, to ,nd,
space between degree_decimal minutes to no space
change nutrient names to chemical symbols
added toplevel to put all three cruises in the same object
got rid of extra lines in ACTII
fixed bad lat/lon points in each cruise with PI input

Methods & Sampling

The water samples were collected with a Seabird 911+ CTD.

Nutrient concentrations were measured by standard wet chemical methods using a SEAL Analytical AA3 Continuous Segmented Flow Analyzer.

Samples for chlorophyll a concentrations were collected by filtering 100 ml of water through Whatman GF/F filters and stored at -20 ^oC until analysis. To estimate concentrations, the filters were placed into 90% acetone and 40% dimethyl sulfoxide (DMSO) and then the fluorescence in the extract was measured with a Turner Designs 10-AU fluorometer.

The attenuation coefficient was estimated by measuring photosynthetically active radiance with a Biospherical PNF-210 radiometer over a depth profile. In nearly all cases, the downcast and upcast profiles of radiance were indistinguishable and all data were used. When differences between the down and upcasts were apparent, only the downcast data were used.

Data Processing Description

Nutrient concentrations were not processed except for converting raw spectrometric or fluorometric readings to concentrations.

Radiance values at very shallow or very deep depths were excluded from the analysis to calculate the attenuation coefficient when these values were clearly not along the ln (radiance) vs. depth line.

Bacterial Production: Assumes average C per cell = 15 fg and 0.125 nmol-C/pmol of leucine.

Data Files

File
newACT_cruises_rs.csv (Comma Separated Values (.csv), 54.62 KB) MD5:b6c40914994ffdba93181c24f0fce795 Primary data file for dataset ID 565451

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1261359

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
HRS1511	ACT-5	2015-08-17	R/V Hugh R. Sharp	Dr Barbara Campbell (Chief Scientist)	data info
HRS1501	ACT-4	2015-04-11	R/V Hugh R. Sharp	Dr Barbara Campbell (Chief Scientist)	data info
HRS1422	ACT-3	2014-10-31	R/V Hugh R. Sharp	Dr Barbara Campbell (Chief Scientist)	data info
HRS1416	ACT-2	2014-08-27	R/V Hugh R. Sharp	Dr Barbara Campbell (Chief Scientist)	data info
HRS1402	ACT-1	2014-03-18	R/V Hugh R. Sharp	Dr Barbara Campbell (Chief Scientist)	data info

Instruments

CTD Sea-Bird 911

Supplied Name: CTD Seabird 911+

Supplied Description:

Standard Seabird CTD911+

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 Description:

Viruses were counted using a flow cytometer at Xiamen University, following their published method: Horizontal and Vertical Distribution of Marine Virioplankton: A Basin Scale Investigation Based on a Global Cruise. Y. Liang, et al. PLOS ONE www.plosone.org November 2014 9:11; e111634

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
cruise_informal	project name for the cruise	text	cruise_id
cruiseid	official name of the cruise	text	cruise_id
date_local	date of measurement	m/dd/yyyy	date_local
time_local	local time of day	HH:MM	time
lat	the latitude of the CTD or station	decimal degrees	lat
lon	the longitude of the CTD or station; negative means West of Greenwich	decimal degrees	lon
station	sequential cruise station number	number	station
CTD	sequential CTD cast number	number	cast
temp	water temperature	degrees centrigrade	temperature
sal	water salinity	PSU	sal
secchi_depth	depth at which the Secchi disk could no longer be distinguished	meters	depth
PAR	Photosynthetically active radiation; designates the spectral range (wave band) of solar radiation from 400 to 700 nanometers that photosynthetic organisms are able to use in the process of photosynthesis	microEinsteins per square meter per second	PAR
atten	attenuation coefficient	per meter	beam_c
atten_err	error for attenuation coefficient	calculated number	std_err
depth_sample	depth of the sample data	meters	depth
cell_counts	cell counts	cells per milliliter	count
counts_sd	standard deviation of cell counts (i.e.difference from the mean/average)	cells per ml	std_dev
counts_se	standard error of cell counts (taking into account the number of samples tested. Error is used to get a better representation of the deviation/error with larger numbers of samples; such as cell counts where we average 10 fields of view to get a number)	cells per milliliter	std_err
bact_prod	bacterial production of the whole sample	nanograms of Carbon per Liter per hour	production
bact_prod_sd	standard deviation of measurement of bacterial production	nanograms of Carbon per Liter per hour	std_dev
bact_prod_lt_pt8	bacterial production of the part of the sample less than 0.8 microns	nanograms of Carbon per Liter per hour	production
bact_prod_lt_pt8_sd	standard deviation of bacterial production of the part of the sample less than 0.8 microns	nanograms of Carbon per Liter per hour	std_dev
bact_size_frac	percentage of the whole sample that is less than 0.8 microns	percentage	no_bcodmo_term
chla	chlorophyll a concentration	micrograms per liter	chl_a
chla_sd	standard deviation of chlorophyll measurements	micrograms per liter	std_dev
NO3	Nitrate concentration	micromoles per liter	NO3
NO3_sd	standard deviation of Nitrate measurements	micromoles per liter	std_dev
NH4	Ammonium concentration	micromoles per liter	NH4
NH4_sd	standard deviation of Ammonium measurements	micromoles per liter	std_dev
PO4	Phosphate concentration	micromoles per liter	PO4
PO4_sd	standard deviation of Phosphate measurements	micromoles per liter	std_dev
SiO4	Silicate concentration	micromoles per liter	SiO4
SiO4_sd	standard deviation of Silicate measurements	micromoles per liter	std_dev
viral_count	number of viruses in the sample	numbers per milliliter	abundance
viral_count_sd	standard deviation of the count of the number of viruses in the sample	numbers per milliliter	std_dev

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Dataset: Bacterial Growth ACTivity