http://lod.bco-dmo.org/id/dataset/2457
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2009-11-29
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Nutrients, chlorophyll a, and flow cytometry counts of bacteria, Synechococcus, and photosynthetic eucaryotes from 13 cruises on into the Northeast Pacific from 2001-2003 as part of the U.S. GLOBEC program (NEP project)
2012-04-25
publication
2012-04-25
revision
National Oceanographic Data Center (NODC)
2013-10-28
publication
http://accession.nodc.noaa.gov/0113949
Barry Sherr
Oregon State University
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Sherr, B. (2012) Nutrients, chlorophyll a, and flow cytometry counts of bacteria, Synechococcus, and photosynthetic eucaryotes from 13 cruises on into the Northeast Pacific from 2001-2003 as part of the U.S. GLOBEC program (NEP project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2012-04-25 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/2457 [access date]
Rosette Bottle Data (nutrients, chl) fcm Ev & Barry Sherr Flow Cytometry Counts of Bacteria, Synecho, and PEUK Dataset Description: <p><strong>Description:</strong> Also see corresponding CTD data files. Data is from Niskin bottle sampling on cruises in 2001, 2002, and 2003. Data are final. Data are organised by year, cruise, transect, station. Station numbers are included for reference to other cruise data.</p>
<p>E. B. SHERR, NEP-GLOBEC Flow Cytometry data on abundance of heterotrophic bacterial cells: total, high nucleic acid, and low nucleic acid, on abundance of coccoid cyanobacteria, and on abundance of small eukaryotic autotrophic cells.</p>
<p><strong>Publications based on this data set:</strong><br />
Sherr, E.B., Sherr, B.F., Wheeler, P.A. 2005. Distribution of coccoid cyanobacteria and small eukaryotic phytoplankton in the upwelling ecosystem off the Oregon coast during 2001 and 2002. Deep-Sea Research II 52:317-330<br />
Sherr E.B., Sherr B.F., Longnecker K. 2006. Distribution of bacterial abundance and cell-specific nucleic acid content in the Northeast Pacific Ocean. Deep-Sea Research I 53:713-725</p>
<p><em>Last modified: April 25, 2012; May 19, 2006;</em> <em>March 21, 2006</em></p> Methods and Sampling: <p><strong>Sample collection</strong>: During each of 13 GLOBEC NEP-LTOP survey cruises, from March 2001 to September 2003, 4 to 8 stations were sampled along a transect line off Newport, Oregon to 160 kilometers offshore. In March and September 2001, and in April, July and September 2002 and 2003, three to four additional transect lines to the south were also sampled (<a href="http://globec.whoi.edu/images/nep/nep_ltop_stations.gif" target="_blank">Figure 1.</a> ). At each station sampled, water was collected, using 5-liter Niskin bottles mounted on a CTD rosette, for analysis of bacteria and phytoplankton stocks via flow cytometry from 4 to 6 depths in the upper 100 to 150 m. Samples were also collected from the same Niskin bottles as part of the LTOP service program for determination of concentrations of inorganic nutrients and chlorophyll-a. Sensors on the CTD provided profiles of salinity, temperature, and in situ fluorescence at each station.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0000733 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0000733
Funding provided by National Oceanic and Atmospheric Administration (NOAA) Award Number: NA67RJ0151 (NEP)
Funding provided by National Oceanic and Atmospheric Administration (NOAA) Award Number: NA86OP0589 (NEP)
completed
Barry Sherr
Oregon State University
College of Earth, Ocean, and Atmospheric Sciences (CEOAS) Oregon State University 104 CEOAS Admin. Bldg.
Corvallis
OR
97331-5503
USA
sherrb@coas.oregonstate.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
year
cruiseid
transect
station
station_std
depth_w
month_gmt
day_gmt
time_gmt
lat
lon
depth
bact_total_abund
bact_HNA_abund
bact_LNA_abund
FL_ratio_HNAtoLNA
coccus_s
ph_euk_abund
temp
sal
PO4
SIO2
NO3_NO2
chl_a
Niskin Bottle
theme
None, User defined
year
cruise id
transect
station
station_std
depth_w
month_gmt
day_gmt
time_gmt
latitude
longitude
depth
No BCO-DMO term
synechococcus abundance
water temperature at measurement depth
salinity
reactive phosphorus (PO4)
nitrate plus nitrite
chlorophyll a
featureType
BCO-DMO Standard Parameters
Niskin bottle
instrument
BCO-DMO Standard Instruments
W0103B
W0107A
W0109A
W0111B
W0202A
W0204A
W0207A
AT7-21
W0212A
W0302A
W0304A
NH0307A
W0309B
service
Deployment Activity
Northeast Pacific
place
Locations
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
U.S. GLOBal ocean ECosystems dynamics
http://www.usglobec.org/
U.S. GLOBal ocean ECosystems dynamics
U.S. GLOBEC (GLOBal ocean ECosystems dynamics) is a research program organized by oceanographers and fisheries scientists to address the question of how global climate change may affect the abundance and production of animals in the sea.
The U.S. GLOBEC Program currently had major research efforts underway in the Georges Bank / Northwest Atlantic Region, and the Northeast Pacific (with components in the California Current and in the Coastal Gulf of Alaska). U.S. GLOBEC was a major contributor to International GLOBEC efforts in the Southern Ocean and Western Antarctic Peninsula (WAP).
U.S. GLOBEC
largerWorkCitation
program
U.S. GLOBEC Northeast Pacific
http://nepglobec.bco-dmo.org
U.S. GLOBEC Northeast Pacific
<p><strong>Program in a Nutshell</strong></p>
<p><strong>Goal: </strong> To understand the effects of climate variability and climate change on the distribution, abundance and production of marine animals (including commercially important living marine resources) in the eastern North Pacific. To embody this understanding in diagnostic and prognostic ecosystem models, capable of capturing the ecosystem response to major climatic fluctuations.</p>
<p><strong>Approach: </strong>To study the effects of past and present climate variability on the population ecology and population dynamics of marine biota and living marine resources, and to use this information as a proxy for how the ecosystems of the eastern North Pacific may respond to future global climate change. The strong temporal variability in the physical and biological signals of the NEP will be used to examine the biophysical mechanisms through which zooplankton and salmon populations respond to physical forcing and biological interactions in the coastal regions of the two gyres. Annual and interannual variability will be studied directly through <strong>long-term observations</strong> and detailed <strong>process studies</strong>; variability at longer time scales will be examined through <strong>retrospective analysis</strong> of directly measured and proxy data. Coupled <strong>biophysical models</strong> of the ecosystems of these regions will be developed and tested using the process studies and data collected from the long-term observation programs, then further tested and improved by hindcasting selected retrospective data series.</p>
NEP
largerWorkCitation
project
eng; USA
oceans
Northeast Pacific
-126.05
-124.1
41.9
44.6517
2012-04-25
Northeast Pacific Ocean, Gulf of Alaska
0
BCO-DMO catalogue of parameters from Nutrients, chlorophyll a, and flow cytometry counts of bacteria, Synechococcus, and photosynthetic eucaryotes from 13 cruises on into the Northeast Pacific from 2001-2003 as part of the U.S. GLOBEC program (NEP project)
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/9285.rdf
Name: year
Units: dimensionless
Description: <p>Year</p>
http://lod.bco-dmo.org/id/dataset-parameter/9286.rdf
Name: cruiseid
Units: dimensionless
Description: <p>Cruise identifier (e.g. W0302A = R/V Wecoma cruise 0302A).</p>
http://lod.bco-dmo.org/id/dataset-parameter/9287.rdf
Name: transect
Units: dimensionless
Description: <p>Transect identifier.</p>
http://lod.bco-dmo.org/id/dataset-parameter/9288.rdf
Name: station
Units: dimensionless
Description: <p>Station number.</p>
http://lod.bco-dmo.org/id/dataset-parameter/9289.rdf
Name: station_std
Units: dimensionless
Description: <p>Standard station name.</p>
http://lod.bco-dmo.org/id/dataset-parameter/9290.rdf
Name: depth_w
Units: unknown
Description: <p>Bottom depth. </p>
http://lod.bco-dmo.org/id/dataset-parameter/9291.rdf
Name: month_gmt
Units: dimensionless
Description: <p>Month.</p>
http://lod.bco-dmo.org/id/dataset-parameter/9292.rdf
Name: day_gmt
Units: dimensionless
Description: <p>Day of month.</p>
http://lod.bco-dmo.org/id/dataset-parameter/9293.rdf
Name: time_gmt
Units: dimensionless
Description: <p>Time (GMT); 24 hr clock (HHMM).</p>
http://lod.bco-dmo.org/id/dataset-parameter/9294.rdf
Name: lat
Units: decimal degrees
Description: <p>Latitude.</p>
http://lod.bco-dmo.org/id/dataset-parameter/9295.rdf
Name: lon
Units: decimal degrees
Description: <p>Longitude.</p>
http://lod.bco-dmo.org/id/dataset-parameter/9296.rdf
Name: depth
Units: meters
Description: <p>Sample collection depth.</p>
http://lod.bco-dmo.org/id/dataset-parameter/9297.rdf
Name: bact_total_abund
Units: cells per mL
Description: <p>Total abundance of bacteria. Parameter originally named 'bact_total_abund_cellsperml (N1)'.</p>
http://lod.bco-dmo.org/id/dataset-parameter/9298.rdf
Name: bact_HNA_abund
Units: cells per mL
Description: <p>Abundance of HNA (high-nucleic acid content) bacteria. Parameter originally named 'bact_HNA_abund_cellsperml (N2)'.</p>
http://lod.bco-dmo.org/id/dataset-parameter/9299.rdf
Name: bact_LNA_abund
Units: cells per mL
Description: <p>Abundance of LNA (low nucleic acid content) bacteria. Parameter originally named 'bact_LNA_abund_cellsperml (N3)'.</p>
http://lod.bco-dmo.org/id/dataset-parameter/9300.rdf
Name: FL_ratio_HNAtoLNA
Units: dimensionless (ratio)
Description: <p>Ratio of fluorescence of High Nucleic Acid particles to Low Nucleic Acid particles in that sample. Also referred to as 'N4'.</p>
http://lod.bco-dmo.org/id/dataset-parameter/9301.rdf
Name: coccus_s
Units: cells per mL
Description: <p>Abundance of coccoid cyanobacteria (Synechococcus). Original parameter name 'Synecho_abund_perml (N5)'.</p>
http://lod.bco-dmo.org/id/dataset-parameter/9302.rdf
Name: ph_euk_abund
Units: cells per mL
Description: <p>Abundance of photosynthetic eucaryotes. Parameter originally named 'PEUK_abund_perml (N6)'.</p>
http://lod.bco-dmo.org/id/dataset-parameter/9303.rdf
Name: temp
Units: degrees C
Description: <p>Temperature</p>
http://lod.bco-dmo.org/id/dataset-parameter/9304.rdf
Name: sal
Units: psu
Description: <p>Salinity</p>
http://lod.bco-dmo.org/id/dataset-parameter/9305.rdf
Name: PO4
Units: umoles/L
Description: <p>PO4.</p>
http://lod.bco-dmo.org/id/dataset-parameter/9306.rdf
Name: SIO2
Units: umoles/L
Description: <p>SiO2.</p>
http://lod.bco-dmo.org/id/dataset-parameter/9307.rdf
Name: NO3_NO2
Units: umoles/L
Description: <p>Nitrate and Nitrite.</p>
http://lod.bco-dmo.org/id/dataset-parameter/9308.rdf
Name: chl_a
Units: ug/L
Description: <p>chlorophyll</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
212614
https://datadocs.bco-dmo.org/file/JEE1ngjIyBD3mV/fcm.csv
fcm.csv
Primary data file for dataset ID 2457
download
https://osprey.bco-dmo.org/dataset/2457/data/download
download
onLine
dataset
<p><strong>Sample collection</strong>: During each of 13 GLOBEC NEP-LTOP survey cruises, from March 2001 to September 2003, 4 to 8 stations were sampled along a transect line off Newport, Oregon to 160 kilometers offshore. In March and September 2001, and in April, July and September 2002 and 2003, three to four additional transect lines to the south were also sampled (<a href="http://globec.whoi.edu/images/nep/nep_ltop_stations.gif" target="_blank">Figure 1.</a> ). At each station sampled, water was collected, using 5-liter Niskin bottles mounted on a CTD rosette, for analysis of bacteria and phytoplankton stocks via flow cytometry from 4 to 6 depths in the upper 100 to 150 m. Samples were also collected from the same Niskin bottles as part of the LTOP service program for determination of concentrations of inorganic nutrients and chlorophyll-a. Sensors on the CTD provided profiles of salinity, temperature, and in situ fluorescence at each station.</p>
from Cruise: W0103B <p>At each station sampled, water was collected, using 5-liter Niskin bottles mounted on a CTD rosette, for analysis of bacteria and phytoplankton stocks via flow cytometry from 4 to 6 depths in the upper 100 to 150 m. Samples were also collected from the same Niskin bottles as part of the LTOP service program for determination of concentrations of inorganic nutrients and chlorophyll-a. Sensors on the CTD provided profiles of salinity, temperature, and in situ fluorescence at each station.</p>
from Cruise: W0107A <p>At each station sampled, water was collected, using 5-liter Niskin bottles mounted on a CTD rosette, for analysis of bacteria and phytoplankton stocks via flow cytometry from 4 to 6 depths in the upper 100 to 150 m. Samples were also collected from the same Niskin bottles as part of the LTOP service program for determination of concentrations of inorganic nutrients and chlorophyll-a. Sensors on the CTD provided profiles of salinity, temperature, and in situ fluorescence at each station.</p>
from Cruise: W0109A <p>At each station sampled, water was collected, using 5-liter Niskin bottles mounted on a CTD rosette, for analysis of bacteria and phytoplankton stocks via flow cytometry from 4 to 6 depths in the upper 100 to 150 m. Samples were also collected from the same Niskin bottles as part of the LTOP service program for determination of concentrations of inorganic nutrients and chlorophyll-a. Sensors on the CTD provided profiles of salinity, temperature, and in situ fluorescence at each station.</p>
from Cruise: W0111B <p>At each station sampled, water was collected, using 5-liter Niskin bottles mounted on a CTD rosette, for analysis of bacteria and phytoplankton stocks via flow cytometry from 4 to 6 depths in the upper 100 to 150 m. Samples were also collected from the same Niskin bottles as part of the LTOP service program for determination of concentrations of inorganic nutrients and chlorophyll-a. Sensors on the CTD provided profiles of salinity, temperature, and in situ fluorescence at each station.</p>
from Cruise: W0202A <p>At each station sampled, water was collected, using 5-liter Niskin bottles mounted on a CTD rosette, for analysis of bacteria and phytoplankton stocks via flow cytometry from 4 to 6 depths in the upper 100 to 150 m. Samples were also collected from the same Niskin bottles as part of the LTOP service program for determination of concentrations of inorganic nutrients and chlorophyll-a. Sensors on the CTD provided profiles of salinity, temperature, and in situ fluorescence at each station.</p>
from Cruise: W0204A <p>At each station sampled, water was collected, using 5-liter Niskin bottles mounted on a CTD rosette, for analysis of bacteria and phytoplankton stocks via flow cytometry from 4 to 6 depths in the upper 100 to 150 m. Samples were also collected from the same Niskin bottles as part of the LTOP service program for determination of concentrations of inorganic nutrients and chlorophyll-a. Sensors on the CTD provided profiles of salinity, temperature, and in situ fluorescence at each station.</p>
from Cruise: W0207A <p>At each station sampled, water was collected, using 5-liter Niskin bottles mounted on a CTD rosette, for analysis of bacteria and phytoplankton stocks via flow cytometry from 4 to 6 depths in the upper 100 to 150 m. Samples were also collected from the same Niskin bottles as part of the LTOP service program for determination of concentrations of inorganic nutrients and chlorophyll-a. Sensors on the CTD provided profiles of salinity, temperature, and in situ fluorescence at each station.</p>
from Cruise: AT7-21 <p>At each station sampled, water was collected, using 5-liter Niskin bottles mounted on a CTD rosette, for analysis of bacteria and phytoplankton stocks via flow cytometry from 4 to 6 depths in the upper 100 to 150 m. Samples were also collected from the same Niskin bottles as part of the LTOP service program for determination of concentrations of inorganic nutrients and chlorophyll-a. Sensors on the CTD provided profiles of salinity, temperature, and in situ fluorescence at each station.</p>
from Cruise: W0212A <p>At each station sampled, water was collected, using 5-liter Niskin bottles mounted on a CTD rosette, for analysis of bacteria and phytoplankton stocks via flow cytometry from 4 to 6 depths in the upper 100 to 150 m. Samples were also collected from the same Niskin bottles as part of the LTOP service program for determination of concentrations of inorganic nutrients and chlorophyll-a. Sensors on the CTD provided profiles of salinity, temperature, and in situ fluorescence at each station.</p>
from Cruise: W0302A <p>At each station sampled, water was collected, using 5-liter Niskin bottles mounted on a CTD rosette, for analysis of bacteria and phytoplankton stocks via flow cytometry from 4 to 6 depths in the upper 100 to 150 m. Samples were also collected from the same Niskin bottles as part of the LTOP service program for determination of concentrations of inorganic nutrients and chlorophyll-a. Sensors on the CTD provided profiles of salinity, temperature, and in situ fluorescence at each station.</p>
from Cruise: W0304A <p>At each station sampled, water was collected, using 5-liter Niskin bottles mounted on a CTD rosette, for analysis of bacteria and phytoplankton stocks via flow cytometry from 4 to 6 depths in the upper 100 to 150 m. Samples were also collected from the same Niskin bottles as part of the LTOP service program for determination of concentrations of inorganic nutrients and chlorophyll-a. Sensors on the CTD provided profiles of salinity, temperature, and in situ fluorescence at each station.</p>
from Cruise: NH0307A <p>At each station sampled, water was collected, using 5-liter Niskin bottles mounted on a CTD rosette, for analysis of bacteria and phytoplankton stocks via flow cytometry from 4 to 6 depths in the upper 100 to 150 m. Samples were also collected from the same Niskin bottles as part of the LTOP service program for determination of concentrations of inorganic nutrients and chlorophyll-a. Sensors on the CTD provided profiles of salinity, temperature, and in situ fluorescence at each station.</p>
from Cruise: W0309B <p>At each station sampled, water was collected, using 5-liter Niskin bottles mounted on a CTD rosette, for analysis of bacteria and phytoplankton stocks via flow cytometry from 4 to 6 depths in the upper 100 to 150 m. Samples were also collected from the same Niskin bottles as part of the LTOP service program for determination of concentrations of inorganic nutrients and chlorophyll-a. Sensors on the CTD provided profiles of salinity, temperature, and in situ fluorescence at each station.</p>
Specified by the Principal Investigator(s)
<p><strong>Flow Cytometry Methods</strong>:<br />
For flow cytometry samples, 3 ml aliquots were pipetted into 4 ml cryovials and preserved with 0.2% (w/v) final concentration of freshly made paraformaldehyde. The samples were gently mixed and let sit in the dark at room temperature for 10 minutes before quick-freezing and storage in liquid nitrogen. On return of samples to the lab, the cryovials were stored at -80 degrees C until flow cytometric analysis was performed. Duplicate subsamples of seawater for nutrient analyses were collected in acid-washed NalgeneTM 60 ml HDPE bottles and immediately frozen at -20 degrees C for nutrient analysis. For determination of chlorophyll-a concentration, subsamples of whole seawater were vacuum filtered onto 25 mm Whatman GF/F filters, and the filters stored frozen in glass VacutainerTM tubes (-20 degrees C) until processed on shore.</p>
<p><em>Sample analysis</em><br />
Nutrient and chlorophyll-a: Analysis of nutrient and chlorophyll-a concentrations during the GLOBEC cruises were carried out by the NEP-LTOP service group; results are available as a data report (Wetz et al. 2004). Analyses for concentration of nitrate plus nitrite, phosphate and silicic acid (silicate) were performed using a hybrid Technicon AutoAnalyzerII(tm) and Alpkem RFA300(tm) system following protocols modified from Gordon et al. (1995). Standard curves with four different concentrations were run daily at the beginning and end of each run. Fresh standards were made prior to each run by diluting a primary standard with low-nutrient surface seawater. Deionized water (DiW) was used as a blank, and triplicate DiW blanks were run at the beginning and end of each run, to correct for any baseline shifts. In this protocol, the coefficients of variation for duplicates at low nutrient concentrations are typically &lt; 1% (Fleischbein et al., 1999); while at high nutrient concentrations, coefficients of variation are 2-3 % for nitrate and silicate (Corwith and Wheeler 2002). Chlorophyll was extracted for &gt; 12 h in the dark at -20 °C (Parsons et al., 1984) using either 90% acetone or 95% methanol as the solvent. Fluorescence was measured with a Turner Designs(TM) 10-AU fluorometer that had been calibrated with purified chlorophyll-<em>a</em> (Sigma Co.).</p>
<p>Flow cytometric analysis of cell abundances: In the laboratory, samples were thawed and kept on ice in a dark container until run on a Becton-Dickinson FACSCaliber flow cytometer with a 488 nm laser. For enumeration of small sized phytoplankton, 500 µl subsamples were processed as described in Sherr et al. (2005). Populations of coccoid cyanobacteria (Synechococcus or SYN) and of photosynthetic eukaryotes (PEUK) were distinguished by differences in fluorescence in orange (cyanobacteria) and in red (eukaryotic phytoplankton) wavelengths. We have previously determined that 75% to 85% of the red-fluorescing cells in the PEUK region of our cytograms are &lt; 5 µm in size (Sherr et al. 2005). Prochlorococcus appears on the red-fluorescence axis of the flow cytograms to the left of the PEUK region, which was confirmed by a few observations of Prochlorococcus in cytograms of samples collected at a basin station in September 2001.</p>
<p>For heterotrophic bacteria, 250 µl subsamples were diluted with 250 µl of DiW, and stained with SYBR Green I and potassium citrate for 15 min, following the protocol of Marie et al. (1997). Bacterial counts were made during a three minute sample run at low flow rate. Regions were established in cytograms of side scatter and green fluorescence to define bacterial cells with high nucleic acid content (HNA) and low nucleic content (LNA). The cytogram for each sample was individually inspected, and HNA and LNA regions manually moved to conform to the appropriate areas of the bacterial dot-plot. Mean cell-specific SYBR fluorescence was obtained for total bacteria and for HNA and LNA cells, along with abundance of cells within each group. Logical gating in Becton-Dickinson Cell Quest software was used to exclude coccoid cyanobacteria, based on orange fluorescence, from the abundance counts of heterotrophic bacteria.</p>
<p>Each subsample was spiked immediately before processing with a known amount of either 3.0 µm (for phytoplankton) or 1.0 µm (for bacteria) Polysciences Fluoresbrite yellow-green beads from respective stock solutions of beads that had been precalibrated with Becton-Dickinson True-Count beads. The number of beads enumerated in each sample run was used to accurately determine the sample volume processed and thus the abundances of SYN, PEUK, and bacteria.</p>
<p><strong>Notes:</strong><br />
The Thesaurus does not contain the noted fields (N1-N6). The data for N1, N2, N3, N5 and N6 are provided as cells per ml (rather than the thesaurus recommended units of cells per cubic meter). Note N4, the "FL_ratio_HNAtoLNA" is the ratio of fluorescence of High Nucleic Acid particles to Low Nucleic Acid particles in that sample.</p>
<p><strong>References cited:</strong><br />
Corwith, H.L., Wheeler, P.A., 2002. El Nino related variations in nutrient and chlorophyll distributions off Oregon. Progress in Oceanography 54, 361-380. Fleischbein, J., Hill, J., Huyer, A., Smith, R.L., Wheeler P.A., 1999. Hydrographic data from the GLOBEC long-term observation program off Oregon, 1997 and 1998. Data Report 172, Ref. 99-1. OSU.</p>
<p>Gordon, L. I., Jennings, J. C., Ross, A. A., Krest, J. M., 1995. A suggested protocol for continuous flow automated analysis of seawater nutrients (phosphate, nitrate, nitrite and silicic acid) in the WOCE Hydrographic Program and the Joint Global Ocean Fluxes Study, WOCE Operations Manual, WOCE Report No. 68/91. Revision 1995.</p>
<p>Marie, D., Partensky, F., Jacquet, S., Vaulot, D., 1997. Enumeration and cell cycle analysis of natural populations of marine picoplankton by flow cytometry using the nucleic acid stain SYBR Green I. Applied and Environmental Microbiology 63, 186-193.</p>
<p>Parsons, T. R., Maita, Y., Lalli, C.M. 1984. A Manual of Chemical and Biological Methods for Seawater Analysis, 173 pp., Pergamon Press, Oxford, UK.</p>
<p>Sherr, E.B., Sherr, B.F., Wheeler, P.A. 2005. Distribution of coccoid cyanobacteria and small eukaryotic phytoplankton in the upwelling ecosystem off the Oregon coast during 2001 and 2002. Deep-Sea Research II 52:317-330</p>
<p>Wetz, M.S., J. Hill, H. Corwith, and P. A. Wheeler. 2004. Nutrient and Extracted Chlorophyll Data from the GLOBEC Long-Term Observation Program, 1997-2004 Data Report 193</p>
<p><a href="http://globec.whoi.edu/images/nep/nep_ltop_stations.gif" target="_blank">Figure 1.</a> Station locations for the five GLOBEC NEP-LTOP sampling lines off Oregon and northern California: NH - Newport Hydroline off Newport, Oregon; HH - Heceta Head line off Heceta Head, Oregon; FM - Five Mile Point line 20 km south of Coos Bay, Oregon; RR - Rogue River line off the mouth of the Rogue River at Gold Beach, Oregon; and CC - Crescent City line off of Crescent City California just south of the Oregon/California border indicated on the map. Depth contours of 50 m, 200 m, and 2000 m are shown.</p>
from Cruise: W0103B <p>For flow cytometry samples, 3 ml aliquots were pipetted into 4 ml cryovials and preserved with 0.2% (w/v) final concentration of freshly made paraformaldehyde. The samples were gently mixed and let sit in the dark at room temperature for 10 minutes before quick-freezing and storage in liquid nitrogen. On return of samples to the lab, the cryovials were stored at -80 °C until flow cytometric analysis was performed. Duplicate subsamples of seawater for nutrient analyses were collected in acid-washed NalgeneTM 60 ml HDPE bottles and immediately frozen at -20 °C for nutrient analysis. For determination of chlorophyll-a concentration, subsamples of whole seawater were vacuum filtered onto 25 mm Whatman GF/F filters, and the filters stored frozen in glass VacutainerTM tubes (-20 °C) until processed on shore.</p>
<p>Nutrient and chlorophyll-a: Analysis of nutrient and chlorophyll-a concentrations during the GLOBEC cruises were carried out by the NEP-LTOP service group, results are available as a data report (Wetz et al. 2004). Analyses for concentration of nitrate plus nitrite, phosphate and silicic acid (silicate) were performed using a hybrid Technicon AutoAnalyzerII(tm) and Alpkem RFA300(tm) system following protocols modified from Gordon et al. (1995). Standard curves with four different concentrations were run daily at the beginning and end of each run. Fresh standards were made prior to each run by diluting a primary standard with low-nutrient surface seawater. Deionized water (DiW) was used as a blank, and triplicate DiW blanks were run at the beginning and end of each run, to correct for any baseline shifts. In this protocol, the coefficients of variation for duplicates at low nutrient concentrations are typically < 1% (Fleischbein et al., 1999), while at high nutrient concentrations, coefficients of variation are 2-3 % for nitrate and silicate (Corwith and Wheeler 2002). Chlorophyll was extracted for > 12 h in the dark at -20 °C (Parsons et al., 1984) using either 90% acetone or 95% methanol as the solvent. Fluorescence was measured with a Turner Designs(TM) 10-AU fluorometer that had been calibrated with purified chlorophyll-a (Sigma Co.).</p>
<p>Flow cytometric analysis of cell abundances: In the laboratory, samples were thawed and kept on ice in a dark container until run on a Becton-Dickinson FACSCaliber flow cytometer with a 488 nm laser. For enumeration of small sized phytoplankton, 500 µl subsamples were processed as described in Sherr et al. (2005). Populations of coccoid cyanobacteria (Synechococcus or SYN) and of photosynthetic eukaryotes (PEUK) were distinguished by differences in fluorescence in orange (cyanobacteria) and in red (eukaryotic phytoplankton) wavelengths. We have previously determined that 75% to 85% of the red-fluorescing cells in the PEUK region of our cytograms are < 5 µm in size (Sherr et al. 2005). Prochlorococcus appears on the red-fluorescence axis of the flow cytograms to the left of the PEUK region, which was confirmed by a few observations of Prochlorococcus in cytograms of samples collected at a basin station in September 2001.</p>
<p>For heterotrophic bacteria, 250 µl subsamples were diluted with 250 µl of DiW, and stained with SYBR Green I and potassium citrate for 15 min, following the protocol of Marie et al. (1997). Bacterial counts were made during a three minute sample run at low flow rate. Regions were established in cytograms of side scatter and green fluorescence to define bacterial cells with high nucleic acid content (HNA) and low nucleic content (LNA). The cytogram for each sample was individually inspected, and HNA and LNA regions manually moved to conform to the appropriate areas of the bacterial dot-plot. Mean cell-specific SYBR fluorescence was obtained for total bacteria and for HNA and LNA cells, along with abundance of cells within each group. Logical gating in Becton-Dickinson Cell Quest software was used to exclude coccoid cyanobacteria, based on orange fluorescence, from the abundance counts of heterotrophic bacteria.</p>
<p>Each subsample was spiked immediately before processing with a known amount of either 3.0 µm (for phytoplankton) or 1.0 µm (for bacteria) Polysciences Fluoresbrite yellow-green beads from respective stock solutions of beads that had been precalibrated with Becton-Dickinson True-Count beads. The number of beads enumerated in each sample run was used to accurately determine the sample volume processed and thus the abundances of SYN, PEUK, and bacteria.</p>
from Cruise: W0107A <p>For flow cytometry samples, 3 ml aliquots were pipetted into 4 ml cryovials and preserved with 0.2% (w/v) final concentration of freshly made paraformaldehyde. The samples were gently mixed and let sit in the dark at room temperature for 10 minutes before quick-freezing and storage in liquid nitrogen. On return of samples to the lab, the cryovials were stored at -80 °C until flow cytometric analysis was performed. Duplicate subsamples of seawater for nutrient analyses were collected in acid-washed NalgeneTM 60 ml HDPE bottles and immediately frozen at -20 °C for nutrient analysis. For determination of chlorophyll-a concentration, subsamples of whole seawater were vacuum filtered onto 25 mm Whatman GF/F filters, and the filters stored frozen in glass VacutainerTM tubes (-20 °C) until processed on shore.</p>
<p>Nutrient and chlorophyll-a: Analysis of nutrient and chlorophyll-a concentrations during the GLOBEC cruises were carried out by the NEP-LTOP service group, results are available as a data report (Wetz et al. 2004). Analyses for concentration of nitrate plus nitrite, phosphate and silicic acid (silicate) were performed using a hybrid Technicon AutoAnalyzerII(tm) and Alpkem RFA300(tm) system following protocols modified from Gordon et al. (1995). Standard curves with four different concentrations were run daily at the beginning and end of each run. Fresh standards were made prior to each run by diluting a primary standard with low-nutrient surface seawater. Deionized water (DiW) was used as a blank, and triplicate DiW blanks were run at the beginning and end of each run, to correct for any baseline shifts. In this protocol, the coefficients of variation for duplicates at low nutrient concentrations are typically < 1% (Fleischbein et al., 1999), while at high nutrient concentrations, coefficients of variation are 2-3 % for nitrate and silicate (Corwith and Wheeler 2002). Chlorophyll was extracted for > 12 h in the dark at -20 °C (Parsons et al., 1984) using either 90% acetone or 95% methanol as the solvent. Fluorescence was measured with a Turner Designs(TM) 10-AU fluorometer that had been calibrated with purified chlorophyll-a (Sigma Co.).</p>
<p>Flow cytometric analysis of cell abundances: In the laboratory, samples were thawed and kept on ice in a dark container until run on a Becton-Dickinson FACSCaliber flow cytometer with a 488 nm laser. For enumeration of small sized phytoplankton, 500 µl subsamples were processed as described in Sherr et al. (2005). Populations of coccoid cyanobacteria (Synechococcus or SYN) and of photosynthetic eukaryotes (PEUK) were distinguished by differences in fluorescence in orange (cyanobacteria) and in red (eukaryotic phytoplankton) wavelengths. We have previously determined that 75% to 85% of the red-fluorescing cells in the PEUK region of our cytograms are < 5 µm in size (Sherr et al. 2005). Prochlorococcus appears on the red-fluorescence axis of the flow cytograms to the left of the PEUK region, which was confirmed by a few observations of Prochlorococcus in cytograms of samples collected at a basin station in September 2001.</p>
<p>For heterotrophic bacteria, 250 µl subsamples were diluted with 250 µl of DiW, and stained with SYBR Green I and potassium citrate for 15 min, following the protocol of Marie et al. (1997). Bacterial counts were made during a three minute sample run at low flow rate. Regions were established in cytograms of side scatter and green fluorescence to define bacterial cells with high nucleic acid content (HNA) and low nucleic content (LNA). The cytogram for each sample was individually inspected, and HNA and LNA regions manually moved to conform to the appropriate areas of the bacterial dot-plot. Mean cell-specific SYBR fluorescence was obtained for total bacteria and for HNA and LNA cells, along with abundance of cells within each group. Logical gating in Becton-Dickinson Cell Quest software was used to exclude coccoid cyanobacteria, based on orange fluorescence, from the abundance counts of heterotrophic bacteria.</p>
<p>Each subsample was spiked immediately before processing with a known amount of either 3.0 µm (for phytoplankton) or 1.0 µm (for bacteria) Polysciences Fluoresbrite yellow-green beads from respective stock solutions of beads that had been precalibrated with Becton-Dickinson True-Count beads. The number of beads enumerated in each sample run was used to accurately determine the sample volume processed and thus the abundances of SYN, PEUK, and bacteria.</p>
from Cruise: W0109A <p>For flow cytometry samples, 3 ml aliquots were pipetted into 4 ml cryovials and preserved with 0.2% (w/v) final concentration of freshly made paraformaldehyde. The samples were gently mixed and let sit in the dark at room temperature for 10 minutes before quick-freezing and storage in liquid nitrogen. On return of samples to the lab, the cryovials were stored at -80 °C until flow cytometric analysis was performed. Duplicate subsamples of seawater for nutrient analyses were collected in acid-washed NalgeneTM 60 ml HDPE bottles and immediately frozen at -20 °C for nutrient analysis. For determination of chlorophyll-a concentration, subsamples of whole seawater were vacuum filtered onto 25 mm Whatman GF/F filters, and the filters stored frozen in glass VacutainerTM tubes (-20 °C) until processed on shore.</p>
<p>Nutrient and chlorophyll-a: Analysis of nutrient and chlorophyll-a concentrations during the GLOBEC cruises were carried out by the NEP-LTOP service group, results are available as a data report (Wetz et al. 2004). Analyses for concentration of nitrate plus nitrite, phosphate and silicic acid (silicate) were performed using a hybrid Technicon AutoAnalyzerII(tm) and Alpkem RFA300(tm) system following protocols modified from Gordon et al. (1995). Standard curves with four different concentrations were run daily at the beginning and end of each run. Fresh standards were made prior to each run by diluting a primary standard with low-nutrient surface seawater. Deionized water (DiW) was used as a blank, and triplicate DiW blanks were run at the beginning and end of each run, to correct for any baseline shifts. In this protocol, the coefficients of variation for duplicates at low nutrient concentrations are typically < 1% (Fleischbein et al., 1999), while at high nutrient concentrations, coefficients of variation are 2-3 % for nitrate and silicate (Corwith and Wheeler 2002). Chlorophyll was extracted for > 12 h in the dark at -20 °C (Parsons et al., 1984) using either 90% acetone or 95% methanol as the solvent. Fluorescence was measured with a Turner Designs(TM) 10-AU fluorometer that had been calibrated with purified chlorophyll-a (Sigma Co.).</p>
<p>Flow cytometric analysis of cell abundances: In the laboratory, samples were thawed and kept on ice in a dark container until run on a Becton-Dickinson FACSCaliber flow cytometer with a 488 nm laser. For enumeration of small sized phytoplankton, 500 µl subsamples were processed as described in Sherr et al. (2005). Populations of coccoid cyanobacteria (Synechococcus or SYN) and of photosynthetic eukaryotes (PEUK) were distinguished by differences in fluorescence in orange (cyanobacteria) and in red (eukaryotic phytoplankton) wavelengths. We have previously determined that 75% to 85% of the red-fluorescing cells in the PEUK region of our cytograms are < 5 µm in size (Sherr et al. 2005). Prochlorococcus appears on the red-fluorescence axis of the flow cytograms to the left of the PEUK region, which was confirmed by a few observations of Prochlorococcus in cytograms of samples collected at a basin station in September 2001.</p>
<p>For heterotrophic bacteria, 250 µl subsamples were diluted with 250 µl of DiW, and stained with SYBR Green I and potassium citrate for 15 min, following the protocol of Marie et al. (1997). Bacterial counts were made during a three minute sample run at low flow rate. Regions were established in cytograms of side scatter and green fluorescence to define bacterial cells with high nucleic acid content (HNA) and low nucleic content (LNA). The cytogram for each sample was individually inspected, and HNA and LNA regions manually moved to conform to the appropriate areas of the bacterial dot-plot. Mean cell-specific SYBR fluorescence was obtained for total bacteria and for HNA and LNA cells, along with abundance of cells within each group. Logical gating in Becton-Dickinson Cell Quest software was used to exclude coccoid cyanobacteria, based on orange fluorescence, from the abundance counts of heterotrophic bacteria.</p>
<p>Each subsample was spiked immediately before processing with a known amount of either 3.0 µm (for phytoplankton) or 1.0 µm (for bacteria) Polysciences Fluoresbrite yellow-green beads from respective stock solutions of beads that had been precalibrated with Becton-Dickinson True-Count beads. The number of beads enumerated in each sample run was used to accurately determine the sample volume processed and thus the abundances of SYN, PEUK, and bacteria.</p>
from Cruise: W0111B <p>For flow cytometry samples, 3 ml aliquots were pipetted into 4 ml cryovials and preserved with 0.2% (w/v) final concentration of freshly made paraformaldehyde. The samples were gently mixed and let sit in the dark at room temperature for 10 minutes before quick-freezing and storage in liquid nitrogen. On return of samples to the lab, the cryovials were stored at -80 °C until flow cytometric analysis was performed. Duplicate subsamples of seawater for nutrient analyses were collected in acid-washed NalgeneTM 60 ml HDPE bottles and immediately frozen at -20 °C for nutrient analysis. For determination of chlorophyll-a concentration, subsamples of whole seawater were vacuum filtered onto 25 mm Whatman GF/F filters, and the filters stored frozen in glass VacutainerTM tubes (-20 °C) until processed on shore.</p>
<p>Nutrient and chlorophyll-a: Analysis of nutrient and chlorophyll-a concentrations during the GLOBEC cruises were carried out by the NEP-LTOP service group, results are available as a data report (Wetz et al. 2004). Analyses for concentration of nitrate plus nitrite, phosphate and silicic acid (silicate) were performed using a hybrid Technicon AutoAnalyzerII(tm) and Alpkem RFA300(tm) system following protocols modified from Gordon et al. (1995). Standard curves with four different concentrations were run daily at the beginning and end of each run. Fresh standards were made prior to each run by diluting a primary standard with low-nutrient surface seawater. Deionized water (DiW) was used as a blank, and triplicate DiW blanks were run at the beginning and end of each run, to correct for any baseline shifts. In this protocol, the coefficients of variation for duplicates at low nutrient concentrations are typically < 1% (Fleischbein et al., 1999), while at high nutrient concentrations, coefficients of variation are 2-3 % for nitrate and silicate (Corwith and Wheeler 2002). Chlorophyll was extracted for > 12 h in the dark at -20 °C (Parsons et al., 1984) using either 90% acetone or 95% methanol as the solvent. Fluorescence was measured with a Turner Designs(TM) 10-AU fluorometer that had been calibrated with purified chlorophyll-a (Sigma Co.).</p>
<p>Flow cytometric analysis of cell abundances: In the laboratory, samples were thawed and kept on ice in a dark container until run on a Becton-Dickinson FACSCaliber flow cytometer with a 488 nm laser. For enumeration of small sized phytoplankton, 500 µl subsamples were processed as described in Sherr et al. (2005). Populations of coccoid cyanobacteria (Synechococcus or SYN) and of photosynthetic eukaryotes (PEUK) were distinguished by differences in fluorescence in orange (cyanobacteria) and in red (eukaryotic phytoplankton) wavelengths. We have previously determined that 75% to 85% of the red-fluorescing cells in the PEUK region of our cytograms are < 5 µm in size (Sherr et al. 2005). Prochlorococcus appears on the red-fluorescence axis of the flow cytograms to the left of the PEUK region, which was confirmed by a few observations of Prochlorococcus in cytograms of samples collected at a basin station in September 2001.</p>
<p>For heterotrophic bacteria, 250 µl subsamples were diluted with 250 µl of DiW, and stained with SYBR Green I and potassium citrate for 15 min, following the protocol of Marie et al. (1997). Bacterial counts were made during a three minute sample run at low flow rate. Regions were established in cytograms of side scatter and green fluorescence to define bacterial cells with high nucleic acid content (HNA) and low nucleic content (LNA). The cytogram for each sample was individually inspected, and HNA and LNA regions manually moved to conform to the appropriate areas of the bacterial dot-plot. Mean cell-specific SYBR fluorescence was obtained for total bacteria and for HNA and LNA cells, along with abundance of cells within each group. Logical gating in Becton-Dickinson Cell Quest software was used to exclude coccoid cyanobacteria, based on orange fluorescence, from the abundance counts of heterotrophic bacteria.</p>
<p>Each subsample was spiked immediately before processing with a known amount of either 3.0 µm (for phytoplankton) or 1.0 µm (for bacteria) Polysciences Fluoresbrite yellow-green beads from respective stock solutions of beads that had been precalibrated with Becton-Dickinson True-Count beads. The number of beads enumerated in each sample run was used to accurately determine the sample volume processed and thus the abundances of SYN, PEUK, and bacteria.</p>
from Cruise: W0202A <p>For flow cytometry samples, 3 ml aliquots were pipetted into 4 ml cryovials and preserved with 0.2% (w/v) final concentration of freshly made paraformaldehyde. The samples were gently mixed and let sit in the dark at room temperature for 10 minutes before quick-freezing and storage in liquid nitrogen. On return of samples to the lab, the cryovials were stored at -80 °C until flow cytometric analysis was performed. Duplicate subsamples of seawater for nutrient analyses were collected in acid-washed NalgeneTM 60 ml HDPE bottles and immediately frozen at -20 °C for nutrient analysis. For determination of chlorophyll-a concentration, subsamples of whole seawater were vacuum filtered onto 25 mm Whatman GF/F filters, and the filters stored frozen in glass VacutainerTM tubes (-20 °C) until processed on shore.</p>
<p>Nutrient and chlorophyll-a: Analysis of nutrient and chlorophyll-a concentrations during the GLOBEC cruises were carried out by the NEP-LTOP service group, results are available as a data report (Wetz et al. 2004). Analyses for concentration of nitrate plus nitrite, phosphate and silicic acid (silicate) were performed using a hybrid Technicon AutoAnalyzerII(tm) and Alpkem RFA300(tm) system following protocols modified from Gordon et al. (1995). Standard curves with four different concentrations were run daily at the beginning and end of each run. Fresh standards were made prior to each run by diluting a primary standard with low-nutrient surface seawater. Deionized water (DiW) was used as a blank, and triplicate DiW blanks were run at the beginning and end of each run, to correct for any baseline shifts. In this protocol, the coefficients of variation for duplicates at low nutrient concentrations are typically < 1% (Fleischbein et al., 1999), while at high nutrient concentrations, coefficients of variation are 2-3 % for nitrate and silicate (Corwith and Wheeler 2002). Chlorophyll was extracted for > 12 h in the dark at -20 °C (Parsons et al., 1984) using either 90% acetone or 95% methanol as the solvent. Fluorescence was measured with a Turner Designs(TM) 10-AU fluorometer that had been calibrated with purified chlorophyll-a (Sigma Co.).</p>
<p>Flow cytometric analysis of cell abundances: In the laboratory, samples were thawed and kept on ice in a dark container until run on a Becton-Dickinson FACSCaliber flow cytometer with a 488 nm laser. For enumeration of small sized phytoplankton, 500 µl subsamples were processed as described in Sherr et al. (2005). Populations of coccoid cyanobacteria (Synechococcus or SYN) and of photosynthetic eukaryotes (PEUK) were distinguished by differences in fluorescence in orange (cyanobacteria) and in red (eukaryotic phytoplankton) wavelengths. We have previously determined that 75% to 85% of the red-fluorescing cells in the PEUK region of our cytograms are < 5 µm in size (Sherr et al. 2005). Prochlorococcus appears on the red-fluorescence axis of the flow cytograms to the left of the PEUK region, which was confirmed by a few observations of Prochlorococcus in cytograms of samples collected at a basin station in September 2001.</p>
<p>For heterotrophic bacteria, 250 µl subsamples were diluted with 250 µl of DiW, and stained with SYBR Green I and potassium citrate for 15 min, following the protocol of Marie et al. (1997). Bacterial counts were made during a three minute sample run at low flow rate. Regions were established in cytograms of side scatter and green fluorescence to define bacterial cells with high nucleic acid content (HNA) and low nucleic content (LNA). The cytogram for each sample was individually inspected, and HNA and LNA regions manually moved to conform to the appropriate areas of the bacterial dot-plot. Mean cell-specific SYBR fluorescence was obtained for total bacteria and for HNA and LNA cells, along with abundance of cells within each group. Logical gating in Becton-Dickinson Cell Quest software was used to exclude coccoid cyanobacteria, based on orange fluorescence, from the abundance counts of heterotrophic bacteria.</p>
<p>Each subsample was spiked immediately before processing with a known amount of either 3.0 µm (for phytoplankton) or 1.0 µm (for bacteria) Polysciences Fluoresbrite yellow-green beads from respective stock solutions of beads that had been precalibrated with Becton-Dickinson True-Count beads. The number of beads enumerated in each sample run was used to accurately determine the sample volume processed and thus the abundances of SYN, PEUK, and bacteria.</p>
from Cruise: W0204A <p>For flow cytometry samples, 3 ml aliquots were pipetted into 4 ml cryovials and preserved with 0.2% (w/v) final concentration of freshly made paraformaldehyde. The samples were gently mixed and let sit in the dark at room temperature for 10 minutes before quick-freezing and storage in liquid nitrogen. On return of samples to the lab, the cryovials were stored at -80 °C until flow cytometric analysis was performed. Duplicate subsamples of seawater for nutrient analyses were collected in acid-washed NalgeneTM 60 ml HDPE bottles and immediately frozen at -20 °C for nutrient analysis. For determination of chlorophyll-a concentration, subsamples of whole seawater were vacuum filtered onto 25 mm Whatman GF/F filters, and the filters stored frozen in glass VacutainerTM tubes (-20 °C) until processed on shore.</p>
<p>Nutrient and chlorophyll-a: Analysis of nutrient and chlorophyll-a concentrations during the GLOBEC cruises were carried out by the NEP-LTOP service group, results are available as a data report (Wetz et al. 2004). Analyses for concentration of nitrate plus nitrite, phosphate and silicic acid (silicate) were performed using a hybrid Technicon AutoAnalyzerII(tm) and Alpkem RFA300(tm) system following protocols modified from Gordon et al. (1995). Standard curves with four different concentrations were run daily at the beginning and end of each run. Fresh standards were made prior to each run by diluting a primary standard with low-nutrient surface seawater. Deionized water (DiW) was used as a blank, and triplicate DiW blanks were run at the beginning and end of each run, to correct for any baseline shifts. In this protocol, the coefficients of variation for duplicates at low nutrient concentrations are typically < 1% (Fleischbein et al., 1999), while at high nutrient concentrations, coefficients of variation are 2-3 % for nitrate and silicate (Corwith and Wheeler 2002). Chlorophyll was extracted for > 12 h in the dark at -20 °C (Parsons et al., 1984) using either 90% acetone or 95% methanol as the solvent. Fluorescence was measured with a Turner Designs(TM) 10-AU fluorometer that had been calibrated with purified chlorophyll-a (Sigma Co.).</p>
<p>Flow cytometric analysis of cell abundances: In the laboratory, samples were thawed and kept on ice in a dark container until run on a Becton-Dickinson FACSCaliber flow cytometer with a 488 nm laser. For enumeration of small sized phytoplankton, 500 µl subsamples were processed as described in Sherr et al. (2005). Populations of coccoid cyanobacteria (Synechococcus or SYN) and of photosynthetic eukaryotes (PEUK) were distinguished by differences in fluorescence in orange (cyanobacteria) and in red (eukaryotic phytoplankton) wavelengths. We have previously determined that 75% to 85% of the red-fluorescing cells in the PEUK region of our cytograms are < 5 µm in size (Sherr et al. 2005). Prochlorococcus appears on the red-fluorescence axis of the flow cytograms to the left of the PEUK region, which was confirmed by a few observations of Prochlorococcus in cytograms of samples collected at a basin station in September 2001.</p>
<p>For heterotrophic bacteria, 250 µl subsamples were diluted with 250 µl of DiW, and stained with SYBR Green I and potassium citrate for 15 min, following the protocol of Marie et al. (1997). Bacterial counts were made during a three minute sample run at low flow rate. Regions were established in cytograms of side scatter and green fluorescence to define bacterial cells with high nucleic acid content (HNA) and low nucleic content (LNA). The cytogram for each sample was individually inspected, and HNA and LNA regions manually moved to conform to the appropriate areas of the bacterial dot-plot. Mean cell-specific SYBR fluorescence was obtained for total bacteria and for HNA and LNA cells, along with abundance of cells within each group. Logical gating in Becton-Dickinson Cell Quest software was used to exclude coccoid cyanobacteria, based on orange fluorescence, from the abundance counts of heterotrophic bacteria.</p>
<p>Each subsample was spiked immediately before processing with a known amount of either 3.0 µm (for phytoplankton) or 1.0 µm (for bacteria) Polysciences Fluoresbrite yellow-green beads from respective stock solutions of beads that had been precalibrated with Becton-Dickinson True-Count beads. The number of beads enumerated in each sample run was used to accurately determine the sample volume processed and thus the abundances of SYN, PEUK, and bacteria.</p>
from Cruise: W0207A <p>For flow cytometry samples, 3 ml aliquots were pipetted into 4 ml cryovials and preserved with 0.2% (w/v) final concentration of freshly made paraformaldehyde. The samples were gently mixed and let sit in the dark at room temperature for 10 minutes before quick-freezing and storage in liquid nitrogen. On return of samples to the lab, the cryovials were stored at -80 °C until flow cytometric analysis was performed. Duplicate subsamples of seawater for nutrient analyses were collected in acid-washed NalgeneTM 60 ml HDPE bottles and immediately frozen at -20 °C for nutrient analysis. For determination of chlorophyll-a concentration, subsamples of whole seawater were vacuum filtered onto 25 mm Whatman GF/F filters, and the filters stored frozen in glass VacutainerTM tubes (-20 °C) until processed on shore.</p>
<p>Nutrient and chlorophyll-a: Analysis of nutrient and chlorophyll-a concentrations during the GLOBEC cruises were carried out by the NEP-LTOP service group, results are available as a data report (Wetz et al. 2004). Analyses for concentration of nitrate plus nitrite, phosphate and silicic acid (silicate) were performed using a hybrid Technicon AutoAnalyzerII(tm) and Alpkem RFA300(tm) system following protocols modified from Gordon et al. (1995). Standard curves with four different concentrations were run daily at the beginning and end of each run. Fresh standards were made prior to each run by diluting a primary standard with low-nutrient surface seawater. Deionized water (DiW) was used as a blank, and triplicate DiW blanks were run at the beginning and end of each run, to correct for any baseline shifts. In this protocol, the coefficients of variation for duplicates at low nutrient concentrations are typically < 1% (Fleischbein et al., 1999), while at high nutrient concentrations, coefficients of variation are 2-3 % for nitrate and silicate (Corwith and Wheeler 2002). Chlorophyll was extracted for > 12 h in the dark at -20 °C (Parsons et al., 1984) using either 90% acetone or 95% methanol as the solvent. Fluorescence was measured with a Turner Designs(TM) 10-AU fluorometer that had been calibrated with purified chlorophyll-a (Sigma Co.).</p>
<p>Flow cytometric analysis of cell abundances: In the laboratory, samples were thawed and kept on ice in a dark container until run on a Becton-Dickinson FACSCaliber flow cytometer with a 488 nm laser. For enumeration of small sized phytoplankton, 500 µl subsamples were processed as described in Sherr et al. (2005). Populations of coccoid cyanobacteria (Synechococcus or SYN) and of photosynthetic eukaryotes (PEUK) were distinguished by differences in fluorescence in orange (cyanobacteria) and in red (eukaryotic phytoplankton) wavelengths. We have previously determined that 75% to 85% of the red-fluorescing cells in the PEUK region of our cytograms are < 5 µm in size (Sherr et al. 2005). Prochlorococcus appears on the red-fluorescence axis of the flow cytograms to the left of the PEUK region, which was confirmed by a few observations of Prochlorococcus in cytograms of samples collected at a basin station in September 2001.</p>
<p>For heterotrophic bacteria, 250 µl subsamples were diluted with 250 µl of DiW, and stained with SYBR Green I and potassium citrate for 15 min, following the protocol of Marie et al. (1997). Bacterial counts were made during a three minute sample run at low flow rate. Regions were established in cytograms of side scatter and green fluorescence to define bacterial cells with high nucleic acid content (HNA) and low nucleic content (LNA). The cytogram for each sample was individually inspected, and HNA and LNA regions manually moved to conform to the appropriate areas of the bacterial dot-plot. Mean cell-specific SYBR fluorescence was obtained for total bacteria and for HNA and LNA cells, along with abundance of cells within each group. Logical gating in Becton-Dickinson Cell Quest software was used to exclude coccoid cyanobacteria, based on orange fluorescence, from the abundance counts of heterotrophic bacteria.</p>
<p>Each subsample was spiked immediately before processing with a known amount of either 3.0 µm (for phytoplankton) or 1.0 µm (for bacteria) Polysciences Fluoresbrite yellow-green beads from respective stock solutions of beads that had been precalibrated with Becton-Dickinson True-Count beads. The number of beads enumerated in each sample run was used to accurately determine the sample volume processed and thus the abundances of SYN, PEUK, and bacteria.</p>
from Cruise: AT7-21 <p>For flow cytometry samples, 3 ml aliquots were pipetted into 4 ml cryovials and preserved with 0.2% (w/v) final concentration of freshly made paraformaldehyde. The samples were gently mixed and let sit in the dark at room temperature for 10 minutes before quick-freezing and storage in liquid nitrogen. On return of samples to the lab, the cryovials were stored at -80 °C until flow cytometric analysis was performed. Duplicate subsamples of seawater for nutrient analyses were collected in acid-washed NalgeneTM 60 ml HDPE bottles and immediately frozen at -20 °C for nutrient analysis. For determination of chlorophyll-a concentration, subsamples of whole seawater were vacuum filtered onto 25 mm Whatman GF/F filters, and the filters stored frozen in glass VacutainerTM tubes (-20 °C) until processed on shore.</p>
<p>Nutrient and chlorophyll-a: Analysis of nutrient and chlorophyll-a concentrations during the GLOBEC cruises were carried out by the NEP-LTOP service group, results are available as a data report (Wetz et al. 2004). Analyses for concentration of nitrate plus nitrite, phosphate and silicic acid (silicate) were performed using a hybrid Technicon AutoAnalyzerII(tm) and Alpkem RFA300(tm) system following protocols modified from Gordon et al. (1995). Standard curves with four different concentrations were run daily at the beginning and end of each run. Fresh standards were made prior to each run by diluting a primary standard with low-nutrient surface seawater. Deionized water (DiW) was used as a blank, and triplicate DiW blanks were run at the beginning and end of each run, to correct for any baseline shifts. In this protocol, the coefficients of variation for duplicates at low nutrient concentrations are typically < 1% (Fleischbein et al., 1999), while at high nutrient concentrations, coefficients of variation are 2-3 % for nitrate and silicate (Corwith and Wheeler 2002). Chlorophyll was extracted for > 12 h in the dark at -20 °C (Parsons et al., 1984) using either 90% acetone or 95% methanol as the solvent. Fluorescence was measured with a Turner Designs(TM) 10-AU fluorometer that had been calibrated with purified chlorophyll-a (Sigma Co.).</p>
<p>Flow cytometric analysis of cell abundances: In the laboratory, samples were thawed and kept on ice in a dark container until run on a Becton-Dickinson FACSCaliber flow cytometer with a 488 nm laser. For enumeration of small sized phytoplankton, 500 µl subsamples were processed as described in Sherr et al. (2005). Populations of coccoid cyanobacteria (Synechococcus or SYN) and of photosynthetic eukaryotes (PEUK) were distinguished by differences in fluorescence in orange (cyanobacteria) and in red (eukaryotic phytoplankton) wavelengths. We have previously determined that 75% to 85% of the red-fluorescing cells in the PEUK region of our cytograms are < 5 µm in size (Sherr et al. 2005). Prochlorococcus appears on the red-fluorescence axis of the flow cytograms to the left of the PEUK region, which was confirmed by a few observations of Prochlorococcus in cytograms of samples collected at a basin station in September 2001.</p>
<p>For heterotrophic bacteria, 250 µl subsamples were diluted with 250 µl of DiW, and stained with SYBR Green I and potassium citrate for 15 min, following the protocol of Marie et al. (1997). Bacterial counts were made during a three minute sample run at low flow rate. Regions were established in cytograms of side scatter and green fluorescence to define bacterial cells with high nucleic acid content (HNA) and low nucleic content (LNA). The cytogram for each sample was individually inspected, and HNA and LNA regions manually moved to conform to the appropriate areas of the bacterial dot-plot. Mean cell-specific SYBR fluorescence was obtained for total bacteria and for HNA and LNA cells, along with abundance of cells within each group. Logical gating in Becton-Dickinson Cell Quest software was used to exclude coccoid cyanobacteria, based on orange fluorescence, from the abundance counts of heterotrophic bacteria.</p>
<p>Each subsample was spiked immediately before processing with a known amount of either 3.0 µm (for phytoplankton) or 1.0 µm (for bacteria) Polysciences Fluoresbrite yellow-green beads from respective stock solutions of beads that had been precalibrated with Becton-Dickinson True-Count beads. The number of beads enumerated in each sample run was used to accurately determine the sample volume processed and thus the abundances of SYN, PEUK, and bacteria.</p>
from Cruise: W0212A <p>For flow cytometry samples, 3 ml aliquots were pipetted into 4 ml cryovials and preserved with 0.2% (w/v) final concentration of freshly made paraformaldehyde. The samples were gently mixed and let sit in the dark at room temperature for 10 minutes before quick-freezing and storage in liquid nitrogen. On return of samples to the lab, the cryovials were stored at -80 °C until flow cytometric analysis was performed. Duplicate subsamples of seawater for nutrient analyses were collected in acid-washed NalgeneTM 60 ml HDPE bottles and immediately frozen at -20 °C for nutrient analysis. For determination of chlorophyll-a concentration, subsamples of whole seawater were vacuum filtered onto 25 mm Whatman GF/F filters, and the filters stored frozen in glass VacutainerTM tubes (-20 °C) until processed on shore.</p>
<p>Nutrient and chlorophyll-a: Analysis of nutrient and chlorophyll-a concentrations during the GLOBEC cruises were carried out by the NEP-LTOP service group, results are available as a data report (Wetz et al. 2004). Analyses for concentration of nitrate plus nitrite, phosphate and silicic acid (silicate) were performed using a hybrid Technicon AutoAnalyzerII(tm) and Alpkem RFA300(tm) system following protocols modified from Gordon et al. (1995). Standard curves with four different concentrations were run daily at the beginning and end of each run. Fresh standards were made prior to each run by diluting a primary standard with low-nutrient surface seawater. Deionized water (DiW) was used as a blank, and triplicate DiW blanks were run at the beginning and end of each run, to correct for any baseline shifts. In this protocol, the coefficients of variation for duplicates at low nutrient concentrations are typically < 1% (Fleischbein et al., 1999), while at high nutrient concentrations, coefficients of variation are 2-3 % for nitrate and silicate (Corwith and Wheeler 2002). Chlorophyll was extracted for > 12 h in the dark at -20 °C (Parsons et al., 1984) using either 90% acetone or 95% methanol as the solvent. Fluorescence was measured with a Turner Designs(TM) 10-AU fluorometer that had been calibrated with purified chlorophyll-a (Sigma Co.).</p>
<p>Flow cytometric analysis of cell abundances: In the laboratory, samples were thawed and kept on ice in a dark container until run on a Becton-Dickinson FACSCaliber flow cytometer with a 488 nm laser. For enumeration of small sized phytoplankton, 500 µl subsamples were processed as described in Sherr et al. (2005). Populations of coccoid cyanobacteria (Synechococcus or SYN) and of photosynthetic eukaryotes (PEUK) were distinguished by differences in fluorescence in orange (cyanobacteria) and in red (eukaryotic phytoplankton) wavelengths. We have previously determined that 75% to 85% of the red-fluorescing cells in the PEUK region of our cytograms are < 5 µm in size (Sherr et al. 2005). Prochlorococcus appears on the red-fluorescence axis of the flow cytograms to the left of the PEUK region, which was confirmed by a few observations of Prochlorococcus in cytograms of samples collected at a basin station in September 2001.</p>
<p>For heterotrophic bacteria, 250 µl subsamples were diluted with 250 µl of DiW, and stained with SYBR Green I and potassium citrate for 15 min, following the protocol of Marie et al. (1997). Bacterial counts were made during a three minute sample run at low flow rate. Regions were established in cytograms of side scatter and green fluorescence to define bacterial cells with high nucleic acid content (HNA) and low nucleic content (LNA). The cytogram for each sample was individually inspected, and HNA and LNA regions manually moved to conform to the appropriate areas of the bacterial dot-plot. Mean cell-specific SYBR fluorescence was obtained for total bacteria and for HNA and LNA cells, along with abundance of cells within each group. Logical gating in Becton-Dickinson Cell Quest software was used to exclude coccoid cyanobacteria, based on orange fluorescence, from the abundance counts of heterotrophic bacteria.</p>
<p>Each subsample was spiked immediately before processing with a known amount of either 3.0 µm (for phytoplankton) or 1.0 µm (for bacteria) Polysciences Fluoresbrite yellow-green beads from respective stock solutions of beads that had been precalibrated with Becton-Dickinson True-Count beads. The number of beads enumerated in each sample run was used to accurately determine the sample volume processed and thus the abundances of SYN, PEUK, and bacteria.</p>
from Cruise: W0302A <p>For flow cytometry samples, 3 ml aliquots were pipetted into 4 ml cryovials and preserved with 0.2% (w/v) final concentration of freshly made paraformaldehyde. The samples were gently mixed and let sit in the dark at room temperature for 10 minutes before quick-freezing and storage in liquid nitrogen. On return of samples to the lab, the cryovials were stored at -80 °C until flow cytometric analysis was performed. Duplicate subsamples of seawater for nutrient analyses were collected in acid-washed NalgeneTM 60 ml HDPE bottles and immediately frozen at -20 °C for nutrient analysis. For determination of chlorophyll-a concentration, subsamples of whole seawater were vacuum filtered onto 25 mm Whatman GF/F filters, and the filters stored frozen in glass VacutainerTM tubes (-20 °C) until processed on shore.</p>
<p>Nutrient and chlorophyll-a: Analysis of nutrient and chlorophyll-a concentrations during the GLOBEC cruises were carried out by the NEP-LTOP service group, results are available as a data report (Wetz et al. 2004). Analyses for concentration of nitrate plus nitrite, phosphate and silicic acid (silicate) were performed using a hybrid Technicon AutoAnalyzerII(tm) and Alpkem RFA300(tm) system following protocols modified from Gordon et al. (1995). Standard curves with four different concentrations were run daily at the beginning and end of each run. Fresh standards were made prior to each run by diluting a primary standard with low-nutrient surface seawater. Deionized water (DiW) was used as a blank, and triplicate DiW blanks were run at the beginning and end of each run, to correct for any baseline shifts. In this protocol, the coefficients of variation for duplicates at low nutrient concentrations are typically < 1% (Fleischbein et al., 1999), while at high nutrient concentrations, coefficients of variation are 2-3 % for nitrate and silicate (Corwith and Wheeler 2002). Chlorophyll was extracted for > 12 h in the dark at -20 °C (Parsons et al., 1984) using either 90% acetone or 95% methanol as the solvent. Fluorescence was measured with a Turner Designs(TM) 10-AU fluorometer that had been calibrated with purified chlorophyll-a (Sigma Co.).</p>
<p>Flow cytometric analysis of cell abundances: In the laboratory, samples were thawed and kept on ice in a dark container until run on a Becton-Dickinson FACSCaliber flow cytometer with a 488 nm laser. For enumeration of small sized phytoplankton, 500 µl subsamples were processed as described in Sherr et al. (2005). Populations of coccoid cyanobacteria (Synechococcus or SYN) and of photosynthetic eukaryotes (PEUK) were distinguished by differences in fluorescence in orange (cyanobacteria) and in red (eukaryotic phytoplankton) wavelengths. We have previously determined that 75% to 85% of the red-fluorescing cells in the PEUK region of our cytograms are < 5 µm in size (Sherr et al. 2005). Prochlorococcus appears on the red-fluorescence axis of the flow cytograms to the left of the PEUK region, which was confirmed by a few observations of Prochlorococcus in cytograms of samples collected at a basin station in September 2001.</p>
<p>For heterotrophic bacteria, 250 µl subsamples were diluted with 250 µl of DiW, and stained with SYBR Green I and potassium citrate for 15 min, following the protocol of Marie et al. (1997). Bacterial counts were made during a three minute sample run at low flow rate. Regions were established in cytograms of side scatter and green fluorescence to define bacterial cells with high nucleic acid content (HNA) and low nucleic content (LNA). The cytogram for each sample was individually inspected, and HNA and LNA regions manually moved to conform to the appropriate areas of the bacterial dot-plot. Mean cell-specific SYBR fluorescence was obtained for total bacteria and for HNA and LNA cells, along with abundance of cells within each group. Logical gating in Becton-Dickinson Cell Quest software was used to exclude coccoid cyanobacteria, based on orange fluorescence, from the abundance counts of heterotrophic bacteria.</p>
<p>Each subsample was spiked immediately before processing with a known amount of either 3.0 µm (for phytoplankton) or 1.0 µm (for bacteria) Polysciences Fluoresbrite yellow-green beads from respective stock solutions of beads that had been precalibrated with Becton-Dickinson True-Count beads. The number of beads enumerated in each sample run was used to accurately determine the sample volume processed and thus the abundances of SYN, PEUK, and bacteria.</p>
from Cruise: W0304A <p>For flow cytometry samples, 3 ml aliquots were pipetted into 4 ml cryovials and preserved with 0.2% (w/v) final concentration of freshly made paraformaldehyde. The samples were gently mixed and let sit in the dark at room temperature for 10 minutes before quick-freezing and storage in liquid nitrogen. On return of samples to the lab, the cryovials were stored at -80 °C until flow cytometric analysis was performed. Duplicate subsamples of seawater for nutrient analyses were collected in acid-washed NalgeneTM 60 ml HDPE bottles and immediately frozen at -20 °C for nutrient analysis. For determination of chlorophyll-a concentration, subsamples of whole seawater were vacuum filtered onto 25 mm Whatman GF/F filters, and the filters stored frozen in glass VacutainerTM tubes (-20 °C) until processed on shore.</p>
<p>Nutrient and chlorophyll-a: Analysis of nutrient and chlorophyll-a concentrations during the GLOBEC cruises were carried out by the NEP-LTOP service group, results are available as a data report (Wetz et al. 2004). Analyses for concentration of nitrate plus nitrite, phosphate and silicic acid (silicate) were performed using a hybrid Technicon AutoAnalyzerII(tm) and Alpkem RFA300(tm) system following protocols modified from Gordon et al. (1995). Standard curves with four different concentrations were run daily at the beginning and end of each run. Fresh standards were made prior to each run by diluting a primary standard with low-nutrient surface seawater. Deionized water (DiW) was used as a blank, and triplicate DiW blanks were run at the beginning and end of each run, to correct for any baseline shifts. In this protocol, the coefficients of variation for duplicates at low nutrient concentrations are typically < 1% (Fleischbein et al., 1999), while at high nutrient concentrations, coefficients of variation are 2-3 % for nitrate and silicate (Corwith and Wheeler 2002). Chlorophyll was extracted for > 12 h in the dark at -20 °C (Parsons et al., 1984) using either 90% acetone or 95% methanol as the solvent. Fluorescence was measured with a Turner Designs(TM) 10-AU fluorometer that had been calibrated with purified chlorophyll-a (Sigma Co.).</p>
<p>Flow cytometric analysis of cell abundances: In the laboratory, samples were thawed and kept on ice in a dark container until run on a Becton-Dickinson FACSCaliber flow cytometer with a 488 nm laser. For enumeration of small sized phytoplankton, 500 µl subsamples were processed as described in Sherr et al. (2005). Populations of coccoid cyanobacteria (Synechococcus or SYN) and of photosynthetic eukaryotes (PEUK) were distinguished by differences in fluorescence in orange (cyanobacteria) and in red (eukaryotic phytoplankton) wavelengths. We have previously determined that 75% to 85% of the red-fluorescing cells in the PEUK region of our cytograms are < 5 µm in size (Sherr et al. 2005). Prochlorococcus appears on the red-fluorescence axis of the flow cytograms to the left of the PEUK region, which was confirmed by a few observations of Prochlorococcus in cytograms of samples collected at a basin station in September 2001.</p>
<p>For heterotrophic bacteria, 250 µl subsamples were diluted with 250 µl of DiW, and stained with SYBR Green I and potassium citrate for 15 min, following the protocol of Marie et al. (1997). Bacterial counts were made during a three minute sample run at low flow rate. Regions were established in cytograms of side scatter and green fluorescence to define bacterial cells with high nucleic acid content (HNA) and low nucleic content (LNA). The cytogram for each sample was individually inspected, and HNA and LNA regions manually moved to conform to the appropriate areas of the bacterial dot-plot. Mean cell-specific SYBR fluorescence was obtained for total bacteria and for HNA and LNA cells, along with abundance of cells within each group. Logical gating in Becton-Dickinson Cell Quest software was used to exclude coccoid cyanobacteria, based on orange fluorescence, from the abundance counts of heterotrophic bacteria.</p>
<p>Each subsample was spiked immediately before processing with a known amount of either 3.0 µm (for phytoplankton) or 1.0 µm (for bacteria) Polysciences Fluoresbrite yellow-green beads from respective stock solutions of beads that had been precalibrated with Becton-Dickinson True-Count beads. The number of beads enumerated in each sample run was used to accurately determine the sample volume processed and thus the abundances of SYN, PEUK, and bacteria.</p>
from Cruise: NH0307A <p>For flow cytometry samples, 3 ml aliquots were pipetted into 4 ml cryovials and preserved with 0.2% (w/v) final concentration of freshly made paraformaldehyde. The samples were gently mixed and let sit in the dark at room temperature for 10 minutes before quick-freezing and storage in liquid nitrogen. On return of samples to the lab, the cryovials were stored at -80 °C until flow cytometric analysis was performed. Duplicate subsamples of seawater for nutrient analyses were collected in acid-washed NalgeneTM 60 ml HDPE bottles and immediately frozen at -20 °C for nutrient analysis. For determination of chlorophyll-a concentration, subsamples of whole seawater were vacuum filtered onto 25 mm Whatman GF/F filters, and the filters stored frozen in glass VacutainerTM tubes (-20 °C) until processed on shore.</p>
<p>Nutrient and chlorophyll-a: Analysis of nutrient and chlorophyll-a concentrations during the GLOBEC cruises were carried out by the NEP-LTOP service group, results are available as a data report (Wetz et al. 2004). Analyses for concentration of nitrate plus nitrite, phosphate and silicic acid (silicate) were performed using a hybrid Technicon AutoAnalyzerII(tm) and Alpkem RFA300(tm) system following protocols modified from Gordon et al. (1995). Standard curves with four different concentrations were run daily at the beginning and end of each run. Fresh standards were made prior to each run by diluting a primary standard with low-nutrient surface seawater. Deionized water (DiW) was used as a blank, and triplicate DiW blanks were run at the beginning and end of each run, to correct for any baseline shifts. In this protocol, the coefficients of variation for duplicates at low nutrient concentrations are typically < 1% (Fleischbein et al., 1999), while at high nutrient concentrations, coefficients of variation are 2-3 % for nitrate and silicate (Corwith and Wheeler 2002). Chlorophyll was extracted for > 12 h in the dark at -20 °C (Parsons et al., 1984) using either 90% acetone or 95% methanol as the solvent. Fluorescence was measured with a Turner Designs(TM) 10-AU fluorometer that had been calibrated with purified chlorophyll-a (Sigma Co.).</p>
<p>Flow cytometric analysis of cell abundances: In the laboratory, samples were thawed and kept on ice in a dark container until run on a Becton-Dickinson FACSCaliber flow cytometer with a 488 nm laser. For enumeration of small sized phytoplankton, 500 µl subsamples were processed as described in Sherr et al. (2005). Populations of coccoid cyanobacteria (Synechococcus or SYN) and of photosynthetic eukaryotes (PEUK) were distinguished by differences in fluorescence in orange (cyanobacteria) and in red (eukaryotic phytoplankton) wavelengths. We have previously determined that 75% to 85% of the red-fluorescing cells in the PEUK region of our cytograms are < 5 µm in size (Sherr et al. 2005). Prochlorococcus appears on the red-fluorescence axis of the flow cytograms to the left of the PEUK region, which was confirmed by a few observations of Prochlorococcus in cytograms of samples collected at a basin station in September 2001.</p>
<p>For heterotrophic bacteria, 250 µl subsamples were diluted with 250 µl of DiW, and stained with SYBR Green I and potassium citrate for 15 min, following the protocol of Marie et al. (1997). Bacterial counts were made during a three minute sample run at low flow rate. Regions were established in cytograms of side scatter and green fluorescence to define bacterial cells with high nucleic acid content (HNA) and low nucleic content (LNA). The cytogram for each sample was individually inspected, and HNA and LNA regions manually moved to conform to the appropriate areas of the bacterial dot-plot. Mean cell-specific SYBR fluorescence was obtained for total bacteria and for HNA and LNA cells, along with abundance of cells within each group. Logical gating in Becton-Dickinson Cell Quest software was used to exclude coccoid cyanobacteria, based on orange fluorescence, from the abundance counts of heterotrophic bacteria.</p>
<p>Each subsample was spiked immediately before processing with a known amount of either 3.0 µm (for phytoplankton) or 1.0 µm (for bacteria) Polysciences Fluoresbrite yellow-green beads from respective stock solutions of beads that had been precalibrated with Becton-Dickinson True-Count beads. The number of beads enumerated in each sample run was used to accurately determine the sample volume processed and thus the abundances of SYN, PEUK, and bacteria.</p>
from Cruise: W0309B <p>For flow cytometry samples, 3 ml aliquots were pipetted into 4 ml cryovials and preserved with 0.2% (w/v) final concentration of freshly made paraformaldehyde. The samples were gently mixed and let sit in the dark at room temperature for 10 minutes before quick-freezing and storage in liquid nitrogen. On return of samples to the lab, the cryovials were stored at -80 °C until flow cytometric analysis was performed. Duplicate subsamples of seawater for nutrient analyses were collected in acid-washed NalgeneTM 60 ml HDPE bottles and immediately frozen at -20 °C for nutrient analysis. For determination of chlorophyll-a concentration, subsamples of whole seawater were vacuum filtered onto 25 mm Whatman GF/F filters, and the filters stored frozen in glass VacutainerTM tubes (-20 °C) until processed on shore.</p>
<p>Nutrient and chlorophyll-a: Analysis of nutrient and chlorophyll-a concentrations during the GLOBEC cruises were carried out by the NEP-LTOP service group, results are available as a data report (Wetz et al. 2004). Analyses for concentration of nitrate plus nitrite, phosphate and silicic acid (silicate) were performed using a hybrid Technicon AutoAnalyzerII(tm) and Alpkem RFA300(tm) system following protocols modified from Gordon et al. (1995). Standard curves with four different concentrations were run daily at the beginning and end of each run. Fresh standards were made prior to each run by diluting a primary standard with low-nutrient surface seawater. Deionized water (DiW) was used as a blank, and triplicate DiW blanks were run at the beginning and end of each run, to correct for any baseline shifts. In this protocol, the coefficients of variation for duplicates at low nutrient concentrations are typically < 1% (Fleischbein et al., 1999), while at high nutrient concentrations, coefficients of variation are 2-3 % for nitrate and silicate (Corwith and Wheeler 2002). Chlorophyll was extracted for > 12 h in the dark at -20 °C (Parsons et al., 1984) using either 90% acetone or 95% methanol as the solvent. Fluorescence was measured with a Turner Designs(TM) 10-AU fluorometer that had been calibrated with purified chlorophyll-a (Sigma Co.).</p>
<p>Flow cytometric analysis of cell abundances: In the laboratory, samples were thawed and kept on ice in a dark container until run on a Becton-Dickinson FACSCaliber flow cytometer with a 488 nm laser. For enumeration of small sized phytoplankton, 500 µl subsamples were processed as described in Sherr et al. (2005). Populations of coccoid cyanobacteria (Synechococcus or SYN) and of photosynthetic eukaryotes (PEUK) were distinguished by differences in fluorescence in orange (cyanobacteria) and in red (eukaryotic phytoplankton) wavelengths. We have previously determined that 75% to 85% of the red-fluorescing cells in the PEUK region of our cytograms are < 5 µm in size (Sherr et al. 2005). Prochlorococcus appears on the red-fluorescence axis of the flow cytograms to the left of the PEUK region, which was confirmed by a few observations of Prochlorococcus in cytograms of samples collected at a basin station in September 2001.</p>
<p>For heterotrophic bacteria, 250 µl subsamples were diluted with 250 µl of DiW, and stained with SYBR Green I and potassium citrate for 15 min, following the protocol of Marie et al. (1997). Bacterial counts were made during a three minute sample run at low flow rate. Regions were established in cytograms of side scatter and green fluorescence to define bacterial cells with high nucleic acid content (HNA) and low nucleic content (LNA). The cytogram for each sample was individually inspected, and HNA and LNA regions manually moved to conform to the appropriate areas of the bacterial dot-plot. Mean cell-specific SYBR fluorescence was obtained for total bacteria and for HNA and LNA cells, along with abundance of cells within each group. Logical gating in Becton-Dickinson Cell Quest software was used to exclude coccoid cyanobacteria, based on orange fluorescence, from the abundance counts of heterotrophic bacteria.</p>
<p>Each subsample was spiked immediately before processing with a known amount of either 3.0 µm (for phytoplankton) or 1.0 µm (for bacteria) Polysciences Fluoresbrite yellow-green beads from respective stock solutions of beads that had been precalibrated with Becton-Dickinson True-Count beads. The number of beads enumerated in each sample run was used to accurately determine the sample volume processed and thus the abundances of SYN, PEUK, and bacteria.</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Niskin Bottle
Niskin Bottle
PI Supplied Instrument Name: Niskin Bottle PI Supplied Instrument Description:At each station sampled, water was collected, using 5-liter Niskin bottles mounted on a CTD rosette, for analysis of bacteria and phytoplankton stocks via flow cytometry from 4 to 6 depths in the upper 100 to 150 m. Instrument Name: Niskin bottle Instrument Short Name:Niskin bottle Instrument 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. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/
Cruise: W0103B
W0103B
R/V Wecoma
Community Standard Description
NERC Vocabulary Server
R/V Wecoma
vessel
W0103B
Robert Smith
Oregon State University
http://globec.whoi.edu/nep/reports/ccs_cruises/mar01cr.pdf
Report describing W0103B
Cruise: W0107A
W0107A
R/V Wecoma
Community Standard Description
NERC Vocabulary Server
R/V Wecoma
vessel
W0107A
Adriana Huyer
Oregon State University
http://globec.whoi.edu/nep/reports/ccs_cruises/jul01cr.pdf
Report describing W0107A
Cruise: W0109A
W0109A
R/V Wecoma
Community Standard Description
NERC Vocabulary Server
R/V Wecoma
vessel
W0109A
Robert Smith
Oregon State University
http://globec.whoi.edu/nep/reports/ccs_cruises/sep01cr.pdf
Report describing W0109A
Cruise: W0111B
W0111B
R/V Wecoma
Community Standard Description
NERC Vocabulary Server
R/V Wecoma
vessel
W0111B
Adriana Huyer
Oregon State University
http://globec.whoi.edu/nep/reports/ccs_cruises/nov01cr.pdf
Report describing W0111B
Cruise: W0202A
W0202A
R/V Wecoma
Community Standard Description
NERC Vocabulary Server
R/V Wecoma
vessel
W0202A
Adriana Huyer
Oregon State University
http://globec.whoi.edu/nep/reports/ccs_cruises/feb02cr.pdf
Report describing W0202A
Cruise: W0204A
W0204A
R/V Wecoma
Community Standard Description
NERC Vocabulary Server
R/V Wecoma
vessel
W0204A
Robert Smith
Oregon State University
http://globec.whoi.edu/nep/reports/ccs_cruises/apr02cr.pdf
Report describing W0204A
Cruise: W0207A
W0207A
R/V Wecoma
Community Standard Description
NERC Vocabulary Server
R/V Wecoma
vessel
W0207A
Adriana Huyer
Oregon State University
http://globec.whoi.edu/nep/reports/ccs_cruises/jul02cr.pdf
Report describing W0207A
Cruise: AT7-21
AT7-21
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
AT7-21
Adriana Huyer
Oregon State University
http://globec.whoi.edu/nep/reports/ccs_cruises/sep02cr.pdf
Report describing AT7-21
Cruise: W0212A
W0212A
R/V Wecoma
Community Standard Description
NERC Vocabulary Server
R/V Wecoma
vessel
W0212A
Jane Fleischbein
Oregon State University
http://globec.whoi.edu/nep/reports/ccs_cruises/dec02cr.pdf
Report describing W0212A
Cruise: W0302A
W0302A
R/V Wecoma
Community Standard Description
NERC Vocabulary Server
R/V Wecoma
vessel
W0302A
Robert Smith
Oregon State University
http://globec.whoi.edu/nep/reports/ccs_cruises/feb03cr.pdf
Report describing W0302A
Cruise: W0304A
W0304A
R/V Wecoma
Community Standard Description
NERC Vocabulary Server
R/V Wecoma
vessel
W0304A
Robert Smith
Oregon State University
http://globec.whoi.edu/nep/reports/ccs_cruises/apr03cr.pdf
Report describing W0304A
Cruise: NH0307A
NH0307A
R/V New Horizon
Community Standard Description
International Council for the Exploration of the Sea
R/V New Horizon
vessel
NH0307A
Adriana Huyer
Oregon State University
http://globec.whoi.edu/nep/reports/ccs_cruises/jul03cr.pdf
Report describing NH0307A
Cruise: W0309B
W0309B
R/V Wecoma
Community Standard Description
NERC Vocabulary Server
R/V Wecoma
vessel
W0309B
Adriana Huyer
Oregon State University
http://globec.whoi.edu/nep/reports/ccs_cruises/sep03cr.pdf
Report describing W0309B
R/V Wecoma
Community Standard Description
NERC Vocabulary Server
R/V Wecoma
vessel
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
R/V New Horizon
Community Standard Description
International Council for the Exploration of the Sea
R/V New Horizon
vessel