Dataset: active surface bacteria

Name: Microbial abundance, activity, and nutrient concentrations in Delaware Bay from R/V Hugh R. Sharp HRS090706DK in the Delaware Bay from July 2009 (Active bacteria in surface waters project)
Published: 2013-01-22
Keywords: oceans

Cite This Dataset

Spatial Extent: N:39.861 E:-74.9163 S:38.78 W:-75.5743

Project:

Are abundant bacteria more active than rare bacteria in the Sargasso Sea? (Active bacteria in surface waters)

Principal Investigator:

Dr Barbara Campbell (Clemson University, Clemson)

Co-Principal Investigator:

David L. Kirchman (University of Delaware)

Contact:

David L. Kirchman (University of Delaware)

BCO-DMO Data Manager:

Nancy Copley (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version Date:

2013-01-22

Validated:

Yes

Current State:

Final no updates expected

Microbial abundance, activity, and nutrient concentrations in Delaware Bay from R/V Hugh R. Sharp HRS090706DK in the Delaware Bay from July 2009 (Active bacteria in surface waters project)

Expand/Collapse All

Description

The data set includes salinity, light intensity and attenuation, microbial abundance, microbial heterotrophic activity, and inorganic nutrient concentrations along the salinity gradient of the Delaware estuary in July 2009.

Methods & Sampling

The estuary was sampled with Niskin bottles in a CTD rosette from about 0.5 m. Salinity was taken from the CTD while light intensity at various depths was measured with a Biospherical light meter (model PNF-2102P).

Total microbial abundance and average cell size were determined by epifluorescence microscopy as described previously (Nikrad et al. 2012). The abundance of autotrophic microbes (Synechococcus, picoeukaryotes, and Prochlorococcus) was determined by flow cytometry as previously described (Straza and Kirchman 2011). Incorporation of 3H-leucine was measured in 30 minute incubations using standard methods described elsewhere (Kirchman 2001).

The concentrations of ammonium, nitrate, phosphate, and silicate were measured with a Seal AA3 nutrient autoanalyzer as previously described (Sharp et al. 2009).

Data Processing Description

Light attenuation was calculated from light intensities from linear regression analyses of ln(PAR) vs. depth.

Related files and references:

Kirchman, D. L. 2001. Measuring bacterial biomass production and growth rates from leucine incorporation in natural aquatic environments. Pages 227-237 in J. H. Paul, editor. Marine Microbiology. Academic Press, San Diego.

Nikrad, M. P., M. T. Cottrell, and D. L. Kirchman. 2012. Abundance and Single-Cell Activity of Heterotrophic Bacterial Groups in the Western Arctic Ocean in Summer and Winter. Applied and Environmental Microbiology 78:2402-2409.

Sharp, J. H., K. Yoshiyama, A. E. Parker, M. C. Schwartz, S. E. Curless, A. Y. Beauregard, J. E. Ossolinski, and A. R. Davis. 2009. A biogeochemical view of estuarine eutrophication:Seasonal and spatial trends and correlations in the Delaware Estuary. Estuaries and Coasts 32:1023-1043.

Straza, T. R. A. and D. L. Kirchman. 2011. Single-cell response of bacterial groups to light and other environmental factors in the Delaware Bay, USA. Aquatic Microbial Ecology 62:267-277.

Data Files

File
active_bact.csv (Comma Separated Values (.csv), 3.49 KB) MD5:d7949f1163a723983e22f6aaa71f598e Primary data file for dataset ID 3866

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-0825468

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
HRS090706DK		2009-07-06	R/V Hugh R. Sharp	David L. Kirchman (Chief Scientist)	data info

Instruments

CTD - profiler

Supplied Name: CTD profiler

Supplied Description:

Instrument Type

Generic Name: CTD - profiler

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/130/

Generic Description:

The Conductivity, Temperature, Depth (CTD) unit is an integrated instrument package designed to measure the conductivity, temperature, and pressure (depth) of the water column. The instrument is lowered via cable through the water column. It permits scientists to observe the physical properties in real-time via a conducting cable, which is typically connected to a CTD to a deck unit and computer on a ship. The CTD is often configured with additional optional sensors including fluorometers, transmissometers and/or radiometers. It is often combined with a Rosette of water sampling bottles (e.g. Niskin, GO-FLO) for collecting discrete water samples during the cast.

This term applies to profiling CTDs. For fixed CTDs, see https://www.bco-dmo.org/instrument/869934.

Flow Cytometer

Supplied Description:

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)

Fluorescence Microscope

Supplied Name: 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.

Niskin bottle

Supplied Description:

Instrument Type

Generic Name: Niskin bottle

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/

Generic Description:

A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc.

Nutrient Autoanalyzer

Supplied Description:

Seal AA3 nutrient autoanalyzer as previously described (Sharp et al. 2009)

Instrument Type

Generic Name: Nutrient Autoanalyzer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB04/

Generic Description:

Nutrient Autoanalyzer is a generic term used when specific type, make and model were not specified. In general, a Nutrient Autoanalyzer is an automated flow-thru system for doing nutrient analysis (nitrate, ammonium, orthophosphate, and silicate) on seawater samples.

Photosynthetically Available Radiation Sensor

Supplied Description:

Biospherical light meter (model PNF-2102P)

Profiling Natural Fluorescence Radiometer: Unlike strobe fluorometers, a natural fluorometer measures fluorescence emitted under the ambient light conditions that are driving photosynthesis in situ.

Instrument Type

Generic Name: Photosynthetically Available Radiation Sensor

Acronym: PAR sensor

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/122/

Generic Description:

A PAR sensor measures photosynthetically available (or active) radiation. The sensor measures photon flux density (photons per second per square meter) within the visible wavelength range (typically 400 to 700 nanometers). PAR gives an indication of the total energy available to plants for photosynthesis. This instrument name is used when specific type, make and model are not known.

Secchi Disc

Supplied Description:

Instrument Type

Generic Name: Secchi Disc

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0430/

Generic Description:

Typically, a 16 inch diameter white/black quadrant disc used to measure water optical clarity

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
cruise_id	cruise identification; official R2R name	text	cruise_id
cruise_name	cruise identification; project-based name	text	cruise_name
sta	station identifier	text	station
date_local	local date of sample collection	yyyymmdd	date_local
time_local	local time of sample collection	HH:MM:SS	time_local
lat	latitude; north is positive	decimal degrees	lat
lon	longitude; east is positive	decimal degrees	lon
temp	temperature	degrees Celsius	temp
sal	salinity	dimensionless	sal
PAR	Photosynthetically Available [Active] Radiation; downwelling irradiance	q/cm2/s	PAR
depth_secchi	depth at which a Secchi disk disappears	meters	depth_secchi
atten_secchi	light attenuation from Secchi reading	per meter	no_bcodmo_term
atten_err	light attenuation standard error	per meter	no_bcodmo_term
NO3	nitrate concentration	uM	NO3
NO3_sd	nitration standard deviation	uM	no_bcodmo_term
PO4	phosphate concentration	uM	PO4
PO4_sd	phosphate standard deviation	uM	no_bcodmo_term
NH4	ammonium concentration	uM	NH4
NH4_sd	ammonium standard deviation	uM	no_bcodmo_term
Si	silicate concentration	uM	Si
Si_sd	silicate standard deviation	uM	no_bcodmo_term
chl_a	chlorophyl-a concentration	micrograms/liter	chl_a
chl_a_sd	chlorophyl-a standard deviation	micrograms/liter	no_bcodmo_term
bact_cm3	microbial abundance	cells/ml	bact_abun_sed
bact_cm3_sd	microbial abundance standard deviation	cells/ml	bact_cm3_sd
cell_size	microbial cell size (volume)	micrometers^3	no_bcodmo_term
cell_size_se	microbial cell size standard error	micrometers^3	no_bcodmo_term
bact_aap	percent aerobic anoxygenic phototrophic bacteria of total	percent	no_bcodmo_term
bact_aap_sd	aerobic anoxygenic phototrophic bacteria standard deviation	percent	no_bcodmo_term
Synech	Synechococcus abundance	cells/ml	no_bcodmo_term
PicoEuk	picoeukaryotes abundance	cells/ml	no_bcodmo_term
Prochlo	Prochlorococcus abundance	cells/ml	no_bcodmo_term
leu_incorp	3H-leucine incorporation rate	picoMolar/h	no_bcodmo_term
leu_incorp_sd	3H-leucine incorporation standard deviation	picoMolar/h	no_bcodmo_term

Status message

Database

Contribute Data

Dataset: active surface bacteria