http://lod.bco-dmo.org/id/dataset/2518
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
2009-09-24
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Bacteria abundance and thymidine/leucine incorporation from R/V Thomas G. Thompson TT043, TT045, TT049, TT054 cruises in the Arabian Sea in 1995 (U.S. JGOFS Arabian Sea project)
2002-02-27
publication
2002-02-27
revision
BCO-DMO Linked Data URI
2002-02-27
creation
http://lod.bco-dmo.org/id/dataset/2518
Farooq Azam
University of California-San Diego Scripps
principalInvestigator
Hugh W. Ducklow
Marine Biological Laboratory Ecosystems Center
principalInvestigator
David C. Smith
University of California-San Diego Scripps
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: Azam, F., Ducklow, H. W., Smith, D. C. (2002) Bacteria abundance and thymidine/leucine incorporation from R/V Thomas G. Thompson TT043, TT045, TT049, TT054 cruises in the Arabian Sea in 1995 (U.S. JGOFS Arabian Sea project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version final) Version Date 2002-02-27 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/2518 [access date]
Bacteria abundance and thymidine/leucine incorporation Dataset Description: <p>Bacteria abundance and thymidine/leucine incorporation</p> Methods and Sampling: <p>See Platform deployments for cruise specific documentation</p>
Funding provided by National Science Foundation (NSF) Award Number: unknown Arabian Sea NSF
completed
Farooq Azam
University of California-San Diego Scripps
USA
fazam@ucsd.edu
pointOfContact
Hugh W. Ducklow
Marine Biological Laboratory Ecosystems Center
508 289-7193
LDEO
Palisades
NY
10964
USA
hducklow@ldeo.columbia.edu
pointOfContact
David C. Smith
University of California-San Diego Scripps
401-874-6172
215 South Ferry Road
Narragansett
RI
02882
USA
dcsmith@uri.edu
pointOfContact
asNeeded
Dataset Version: final
Unknown
event
sta
sta_std
cast
bot
press
bact_het_orig
bact_het_se
bact_het_mic
thy_incorp
thy_sd
leuc_incorp
leuc_sd
Niskin Bottle
theme
None, User defined
event
station
standard station
cast
bottle number
water pressure
heterotrophic bacteria abundance
heterotrophic bacteria standard error
heterotrophic bacteria abundance
thymidine incorporation rate
standard deviation of thymidine incorporation rate
leucine incorporation rate
standard deviation of leucine incorporation rate
featureType
BCO-DMO Standard Parameters
Niskin bottle
instrument
BCO-DMO Standard Instruments
TT043
TT045
TT049
TT054
service
Deployment Activity
U.S. JGOFS Arabian Sea
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. Joint Global Ocean Flux Study
http://usjgofs.whoi.edu/
U.S. Joint Global Ocean Flux Study
The United States Joint Global Ocean Flux Study was a national component of international JGOFS and an integral part of global climate change research.
The U.S. launched the Joint Global Ocean Flux Study (JGOFS) in the late 1980s to study the ocean carbon cycle. An ambitious goal was set to understand the controls on the concentrations and fluxes of carbon and associated nutrients in the ocean. A new field of ocean biogeochemistry emerged with an emphasis on quality measurements of carbon system parameters and interdisciplinary field studies of the biological, chemical and physical process which control the ocean carbon cycle. As we studied ocean biogeochemistry, we learned that our simple views of carbon uptake and transport were severely limited, and a new "wave" of ocean science was born. U.S. JGOFS has been supported primarily by the U.S. National Science Foundation in collaboration with the National Oceanic and Atmospheric Administration, the National Aeronautics and Space Administration, the Department of Energy and the Office of Naval Research. U.S. JGOFS, ended in 2005 with the conclusion of the Synthesis and Modeling Project (SMP).
U.S. JGOFS
largerWorkCitation
program
U.S. JGOFS Arabian Sea
http://usjgofs.whoi.edu/research/arabian.html
U.S. JGOFS Arabian Sea
<p>The U.S. Arabian Sea Expedition which began in September 1994 and ended in January 1996, had three major components: a U.S. JGOFS Process Study, supported by the National Science Foundation (NSF); Forced Upper Ocean Dynamics, an Office of Naval Research (ONR) initiative; and shipboard and aircraft measurements supported by the National Aeronautics and Space Administration (NASA). The Expedition consisted of 17 cruises aboard the R/V Thomas Thompson, year-long moored deployments of five instrumented surface buoys and five sediment-trap arrays, aircraft overflights and satellite observations. Of the seventeen ship cruises, six were allocated to repeat process survey cruises, four to SeaSoar mapping cruises, six to mooring and benthic work, and a single calibration cruise which was essentially conducted in transit to the Arabian Sea.</p>
Arabian Sea
largerWorkCitation
project
eng; USA
oceans
U.S. JGOFS Arabian Sea
2002-02-27
Arabian Sea
0
BCO-DMO catalogue of parameters from Bacteria abundance and thymidine/leucine incorporation from R/V Thomas G. Thompson TT043, TT045, TT049, TT054 cruises in the Arabian Sea in 1995 (U.S. JGOFS Arabian Sea 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/9670.rdf
Name: event
Units: YYYYMMDD
Description: <p>event number, from event log</p>
http://lod.bco-dmo.org/id/dataset-parameter/9671.rdf
Name: sta
Units: dimensionless
Description: <p>station number, from event log</p>
http://lod.bco-dmo.org/id/dataset-parameter/9672.rdf
Name: sta_std
Units: dimensionless
Description: <p>Arabian Sea standard station identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/9673.rdf
Name: cast
Units: dimensionless
Description: <p>CTD cast number, from event log consecutive within station</p>
http://lod.bco-dmo.org/id/dataset-parameter/9674.rdf
Name: bot
Units: dimensionless
Description: <p>CTD rosette bottle number</p>
http://lod.bco-dmo.org/id/dataset-parameter/9675.rdf
Name: press
Units: decibars
Description: <p>sample depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/9676.rdf
Name: bact_het_orig
Units: cells/liter *10^9
Description: <p>heterotrophic bacteria abundance, original units; microscopy</p>
http://lod.bco-dmo.org/id/dataset-parameter/9677.rdf
Name: bact_het_se
Units: cells/liter *10^9
Description: <p>standard error for heterotrophic bacteria cell counts; original units</p>
http://lod.bco-dmo.org/id/dataset-parameter/9678.rdf
Name: bact_het_mic
Units: cells/milliliter
Description: <p>heterotrophic bacteria abundance; DMO converted units, microscopy</p>
http://lod.bco-dmo.org/id/dataset-parameter/9679.rdf
Name: thy_incorp
Units: picomoles/liter/hr
Description: <p>thymidine incorporation</p>
http://lod.bco-dmo.org/id/dataset-parameter/9680.rdf
Name: thy_sd
Units: picomoles/liter/hr
Description: <p>standard deviation thymidine incorporation</p>
http://lod.bco-dmo.org/id/dataset-parameter/9681.rdf
Name: leuc_incorp
Units: picomoles/liter/hr
Description: <p>leucine incorporation</p>
http://lod.bco-dmo.org/id/dataset-parameter/9682.rdf
Name: leuc_sd
Units: picomoles/liter/hr
Description: <p>standard deviation leucine incorporation</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
17505
https://datadocs.bco-dmo.org/file/g7ErB09Umy6K0Z/bacteria_TT043.csv
bacteria_TT043.csv
Version July 9, 2001
PI: Farooq Azam and David Smith
of: Scripps Institute of Oceanography
dataset: Bacteria abundance and thymidine/leucine incorporation
cruise: Arabian Sea/TTN-043 - Process Cruise 1
ship: R/V Thomas Thompson
download
18512
https://datadocs.bco-dmo.org/file/B1mxKqYh865OVK/bacteria_TT045.csv
bacteria_TT045.csv
Version February 27, 2002
(previous version July 9, 2001)
PI: Hugh Ducklow
of: Virginia Institute of Marine Science
dataset: Bacterial abundance, cell volume and activity
cruise: Arabian Sea/TTN-045 - Process Cruise #2
ship: R/V Thomas Thompson
PI-provided images:
Surface leucine incorporation
Surface thymidine incorporation
Surface bacterial abundance
Surface mean cell volume
download
21712
https://datadocs.bco-dmo.org/file/rgoJQ1liDpn98O/bacteria_TT049.csv
bacteria_TT049.csv
Version February 27, 2002
(previous version July 9, 2001)
PI: Hugh Ducklow
of: Virginia Institute of Marine Science
dataset: Bacterial abundance, cell volume and activity
cruise: Arabian Sea/TTN-049 - Process Cruise #4
ship: R/V Thomas Thompson
download
17635
https://datadocs.bco-dmo.org/file/0A71lKjIJmN9lk/bacteria_TT054.csv
bacteria_TT054.csv
Version July 9, 2001
PI: Farooq Azam and David Smith
of: Scripps Institute of Oceanography
dataset: Bacteria abundance and thymidine/leucine incorporation
cruise: Arabian Sea/TTN-054 - Process Cruise 7
ship: R/V Thomas Thompson
download
https://osprey.bco-dmo.org/dataset/2518/data/download
download
onLine
dataset
<p>See Platform deployments for cruise specific documentation</p>
from Cruise: TT043 <pre>
<b>PI:</b> Farooq Azam and David Smith
<b>of:</b> Scripps Institute of Oceanography
<b>dataset:</b> Bacteria abundance and thymidine/leucine incorporation
<b>dates:</b> January 09, 1995 to January 31, 1995
<b>location:</b> N: 22.483 S: 10 W: 57.2999 E: 68.75
<b>project/cruise:</b> Arabian Sea/TTN-043 - Process Cruise 1 (Late NE Monsoon)
<b>ship:</b> Thomas Thompson
</pre>
<pre>
Sampling
Seawater samples (250 ml) were taken from the Niskin bottles mounted on
the CTD rosette and transferred directly into brown high-density
polyethylene bottles. The bottles were maintained within 2 degrees C of
the in situ temperature until the start of the incubations or fixing.
</pre>
from Cruise: TT045 <pre>
<b>PI-provided images:</b>
<a href="http://usjgofs.whoi.edu/images/ducklow/surf_leu.gif">Surface leucine incorporation</a>
<a href="http://usjgofs.whoi.edu/images/ducklow/surfthy.gif">Surface thymidine incorporation</a>
<a href="http://usjgofs.whoi.edu/images/ducklow/surfbact.gif">Surface bacterial abundance</a>
<a href="http://usjgofs.whoi.edu/images/ducklow/surfcell.gif">Surface mean cell volume</a>
<b>PI:</b> Hugh Ducklow
<b>of:</b> Virginia Institute of Marine Science
<b>dataset:</b> Bacterial abundance, cell volume, thymidine and leucine incorporation
<b>dates:</b> March 15, 1995 to April 07, 1995
<b>location:</b> N: 22.4858 S: 9.9993 W: 57.3007 E: 68.7532
<b>project/cruise:</b> Arabian Sea/TTN-045 Process Cruise 2 (Spring Intermonsoon)
<b>ship:</b> R/V Thomas Thompson
</pre>
from Cruise: TT049 <pre>
<b>PI:</b> Hugh Ducklow
<b>of:</b> Virginia Institute of Marine Science
<b>dataset:</b> Bacterial abundance, cell volume, thymidine &
leucine incorporation
<b>dates:</b> July 18, 1995 to August 13, 1995
<b>location:</b> N: 22.5268 S: 9.911 W: 57.2997 E: 68.7507
<b>project/cruise:</b> Arabian Sea /TTN-049 Process cruise 4 (Middle SW Monsoon)
<b>ship:</b> R/V Thomas Thompson
</pre>
from Cruise: TT054 <pre>
<b>PI:</b> Farooq Azam and David Smith
<b>of:</b> Scripps Institute of Oceanography
<b>dataset:</b> Bacteria abundance and thymidine/leucine incorporation
<b>dates:</b> December 01, 1995 to December 26, 1995
<b>location:</b> N: 22.5011 S: 9.9789 W: 57.302 E: 68.7849
<b>project/cruise:</b> Arabian Sea/TTN-054 - Process Cruise 7 (Early NE Monsoon)
<b>ship:</b> Thomas Thompson
<pre>
Sampling
Seawater samples (250 ml) were taken from the Niskin bottles mounted on
the CTD rosette and transferred directly into brown high-density
polyethylene bottles. The bottles were maintained within 2 degrees C of
the in situ temperature until the start of the incubations or fixing.
</pre>
Specified by the Principal Investigator(s)
<h2>Methods for the bacterial component of US JGOFS Arabian Sea Process 1 and Process 7 Cruises</h2>
<pre>
Bacterial Abundance
Bacterial abundance was determined by epifluorescence microscopy of
acridine orange- stained bacteria on Nuclepore filters ( Hobbie et al.
1977 ). Samples of between 50 to 100 ml of seawater for bacteria counts
were fixed with 0.2 m-filtered, EM-grade glutaraldehyde (1.25% final
concentration; Ted Pella). Subsamples of 2 to 50 ml were vacuum
filtered (&lt; 150 mm Hg) onto 0.2 m pore size, black, polycarbonate
membrane filters (Nuclepore). During filtration, when a sample volume
had been reduced to 2 ml, 200 l of an 0.2 m-filtered acridine orange
working solution (0.05%) was added to the sample in the tower for a
final concentration of 0.005%. Filtration rate was kept low enough to
allow at least 5 minutes of contact with the stain before filtration
was complete. Blanks were 0.2 m-filtered seawater or deionized,
Milli-Q-treated water fixed and processed in the same manner as the
samples. After filtration, filters were transferred quickly (while
still moist) onto fogged glass slides. Before the filters could dry, a
coverslip with a drop of paraffin oil on the underside was placed over
the filter. Slides were stored at approximately 4 degrees C for less
than 1 day, then transferred to a -20 degrees C freezer for longer term
storage. Bacteria were counted at 1250' magnification by
epifluorescence microscopy with an oil immersion objective. Each
sample was counted until either 20 fields or 200 cells had been
enumerated.
Bacterial Production
Bacterial production was estimated using both the 3H-thymidine (
Fuhrman and Azam 1980; Fuhrman and Azam 1982 ) and the 3H-leucine
(Kirchman et al. 1985 ) incorporation methods as modified for
processing by microcentrifugation by Smith and Azam (1992) . Aliquots
of seawater (1.7 ml) were incubated with 20 nM 3H-leucine or
3H-thymidine in the dark. The length of incubation ranged from 1 to 6
hours depending on the depth from which the sample was collected. The
incubations were terminated with the addition of trichloroacetic acid
(TCA; 5% v/v final). Samples which received the addition of TCA prior
to the radioisotope served as blanks. The samples were centrifuged at
16000 x g for 7 min and the supernatant was removed. The pellet was
washed once with 5% TCA and once with 80% ethanol. Liquid
scintillation cocktail was added directly to the centrifuge tube which
were then radioassayed.
References
Fuhrman, J. A. and F. Azam 1980. Bacterioplankton secondary production
estimates for coastal waters of British Columbia, Antarctica and
California. Appl. Environ. Microbiol. 39: 1085-1095.
Fuhrman, J. A. and F. Azam 1982. Thymidine incorporation as a measure
of heterotrophic bacterioplankton production in marine surface waters:
evaluation and field results. Mar. Biol. 66: 109-120.
Hobbie, J. E., R. J. Daley and S. Jasper 1977. Use of nuclepore
filters for counting bacteria by epifluorescence microscopy. Appl.
Environ. Microbiol. 33: 1225-1228.
Kirchman, D., E. K'Nees and R. Hodson 1985. Leucine incorporation and
its potential as a measure of protein synthesis by bacteria in natural
aquatic systems. Appl. Environ. Microbiol. 49: 599-607.
Smith, D. C. and F. Azam 1992. A simple, economical method for
measuring bacterial protein synthesis rates in seawater using
3H-leucine. Mar. Microb. Food Webs. 6: 107- 114.
</pre>
from Cruise: TT043 <h2>Methods for the bacterial component of US JGOFS Arabian Sea Process 1 and Process 7 Cruises</h2>
<pre>
Bacterial Abundance
Bacterial abundance was determined by epifluorescence microscopy of
acridine orange- stained bacteria on Nuclepore filters ( Hobbie et al.
1977 ). Samples of between 50 to 100 ml of seawater for bacteria counts
were fixed with 0.2 m-filtered, EM-grade glutaraldehyde (1.25% final
concentration; Ted Pella). Subsamples of 2 to 50 ml were vacuum
filtered (< 150 mm Hg) onto 0.2 m pore size, black, polycarbonate
membrane filters (Nuclepore). During filtration, when a sample volume
had been reduced to 2 ml, 200 l of an 0.2 m-filtered acridine orange
working solution (0.05%) was added to the sample in the tower for a
final concentration of 0.005%. Filtration rate was kept low enough to
allow at least 5 minutes of contact with the stain before filtration
was complete. Blanks were 0.2 m-filtered seawater or deionized,
Milli-Q-treated water fixed and processed in the same manner as the
samples. After filtration, filters were transferred quickly (while
still moist) onto fogged glass slides. Before the filters could dry, a
coverslip with a drop of paraffin oil on the underside was placed over
the filter. Slides were stored at approximately 4 degrees C for less
than 1 day, then transferred to a -20 degrees C freezer for longer term
storage. Bacteria were counted at 1250' magnification by
epifluorescence microscopy with an oil immersion objective. Each
sample was counted until either 20 fields or 200 cells had been
enumerated.
Bacterial Production
Bacterial production was estimated using both the 3H-thymidine (
Fuhrman and Azam 1980; Fuhrman and Azam 1982 ) and the 3H-leucine
(Kirchman et al. 1985 ) incorporation methods as modified for
processing by microcentrifugation by Smith and Azam (1992) . Aliquots
of seawater (1.7 ml) were incubated with 20 nM 3H-leucine or
3H-thymidine in the dark. The length of incubation ranged from 1 to 6
hours depending on the depth from which the sample was collected. The
incubations were terminated with the addition of trichloroacetic acid
(TCA; 5% v/v final). Samples which received the addition of TCA prior
to the radioisotope served as blanks. The samples were centrifuged at
16000 x g for 7 min and the supernatant was removed. The pellet was
washed once with 5% TCA and once with 80% ethanol. Liquid
scintillation cocktail was added directly to the centrifuge tube which
were then radioassayed.
References
Fuhrman, J. A. and F. Azam 1980. Bacterioplankton secondary production
estimates for coastal waters of British Columbia, Antarctica and
California. Appl. Environ. Microbiol. 39: 1085-1095.
Fuhrman, J. A. and F. Azam 1982. Thymidine incorporation as a measure
of heterotrophic bacterioplankton production in marine surface waters:
evaluation and field results. Mar. Biol. 66: 109-120.
Hobbie, J. E., R. J. Daley and S. Jasper 1977. Use of nuclepore
filters for counting bacteria by epifluorescence microscopy. Appl.
Environ. Microbiol. 33: 1225-1228.
Kirchman, D., E. K'Nees and R. Hodson 1985. Leucine incorporation and
its potential as a measure of protein synthesis by bacteria in natural
aquatic systems. Appl. Environ. Microbiol. 49: 599-607.
Smith, D. C. and F. Azam 1992. A simple, economical method for
measuring bacterial protein synthesis rates in seawater using
3H-leucine. Mar. Microb. Food Webs. 6: 107- 114.
</pre>
from Cruise: TT045 <pre>
Methods:
Bacteria were enumerated essentially as described in our EqPac data
documentation and the article in the EQPAC I DSR volume. Multiple
images of all samples were acquired, processed and analyzed with Zeiss
software. We used a new algorithm which removed most, but possibly not
all of the prochlorophytes, so these data represent heterotrophic
bacterial counts only. We will be comparing samples with Rob Olson and
David Caron to constrain the bacteria counts. We also include estimates
of the mean volume of cells in each sample.
Bacterial abundance times cell volume yields total biovolume per liter,
an index of bacterial biomass, to which carbon per unit volume factors
can (and will) be applied. All raw images have been archived and can be
made available by separate arrangement.
Bacterial production was estimated by the incorporation of 3H-thymidine
and 3H-leucine into cold, 5% TCA-insoluble extracts, essentially as
described in our earlier JGOFS work, although using the new method of
Smith & Azam (see the Azam data documentation for Process-1).
Production estimates are forthcoming.
Analytical precision for bacterial abundance and cell volume.
We do not routinely perform replicate determinations of bacterial
counts. However, reanalysis of 92 slides from the March series gave
the following coefficients of variation (sd/mean) for bacterial
abundance and cell volume:
property mean st.dev.CV (%) n
- - - - - - - - - - - - -
abundance*0.53 0.061 11.7 92
cell volume 0.037 0.00616.4 92
- - - - - - - - - - - - -
*units for abundance are x 10^9 cells/liter. volumes are um3/cell;
these are mean values for 92 replicate determinations of each
property.
Hugh Ducklow tel 804-642-7180
Virginia Institute of Marine Sciences fax 804-642-7293
Box 1346 email duck@vims.edu
Gloucester Point, VA 23062-1346
</pre>
from Cruise: TT049 <h2>Hugh Ducklow's notes on methodology</h2>
<pre>
Comments:
Incorporation data are only available for stations 13 - 30 as Omani
customs would not allow our isotopes into the country.
Methods:
Bacteria were enumerated essentially as described in our EqPac data
documentation and the article in the EQPAC I DSR volume. Multiple
images of all samples were acquired, processed and analyzed with Zeiss
software. We used a new algorithm which removed most, but possibly not
all of the prochlorophytes, so these data represent heterotrophic
bacterial counts only. We will be comparing samples with Rob Olson and
David Caron to constrain the bacteria counts. We also include estimates
of the mean volume of cells in each sample.
Bacterial abundance times cell volume yields total biovolume per liter,
an index of bacterial biomass, to which carbon per unit volume factors
can (and will) be applied. All raw images have been archived and can be
made available by separate arrangement.
Bacterial production was estimated by the incorporation of 3H-thymidine
and 3H-leucine into cold, 5% TCA-insoluble extracts, essentially as
described in our earlier JGOFS work, although using the new method of
Smith & Azam (see the Azam data documentation for Process-1).
Production estimates are forthcoming.
Analytical precision for bacterial abundance and cell volume.
We do not routinely perform replicate determinations of bacterial
counts. However, reanalysis of 92 slides from the March series gave
the following coefficients of variation (sd/mean) for bacterial
abundance and cell volume:
property mean st.dev. CV (%) n
- - - - - - - - - - - - -
abundance* 0.53 0.061 11.7 92
cell volume 0.037 0.006 16.4 92
- - - - - - - - - - - - -
*units for abundance are x 10^9 cells/liter. volumes are um3/cell;
these are mean values for 92 replicate determinations of each
property.
Hugh Ducklow tel 804-642-7180
Virginia Institute of Marine Sciences fax 804-642-7293
Box 1346 email duck@vims.edu
Gloucester Point, VA 23062-1346
</pre>
from Cruise: TT054 <h2>Methods for the bacterial component of US JGOFS Arabian Sea Process 1 and Process 7 Cruises</h2>
<pre>
Bacterial Abundance
Bacterial abundance was determined by epifluorescence microscopy of
acridine orange- stained bacteria on Nuclepore filters ( Hobbie et al.
1977 ). Samples of between 50 to 100 ml of seawater for bacteria counts
were fixed with 0.2 m-filtered, EM-grade glutaraldehyde (1.25% final
concentration; Ted Pella). Subsamples of 2 to 50 ml were vacuum
filtered (< 150 mm Hg) onto 0.2 m pore size, black, polycarbonate
membrane filters (Nuclepore). During filtration, when a sample volume
had been reduced to 2 ml, 200 l of an 0.2 m-filtered acridine orange
working solution (0.05%) was added to the sample in the tower for a
final concentration of 0.005%. Filtration rate was kept low enough to
allow at least 5 minutes of contact with the stain before filtration
was complete. Blanks were 0.2 m-filtered seawater or deionized,
Milli-Q-treated water fixed and processed in the same manner as the
samples. After filtration, filters were transferred quickly (while
still moist) onto fogged glass slides. Before the filters could dry, a
coverslip with a drop of paraffin oil on the underside was placed over
the filter. Slides were stored at approximately 4 degrees C for less
than 1 day, then transferred to a -20 degrees C freezer for longer term
storage. Bacteria were counted at 1250' magnification by
epifluorescence microscopy with an oil immersion objective. Each
sample was counted until either 20 fields or 200 cells had been
enumerated.
Bacterial Production
Bacterial production was estimated using both the 3H-thymidine (
Fuhrman and Azam 1980; Fuhrman and Azam 1982 ) and the 3H-leucine
(Kirchman et al. 1985 ) incorporation methods as modified for
processing by microcentrifugation by Smith and Azam (1992) . Aliquots
of seawater (1.7 ml) were incubated with 20 nM 3H-leucine or
3H-thymidine in the dark. The length of incubation ranged from 1 to 6
hours depending on the depth from which the sample was collected. The
incubations were terminated with the addition of trichloroacetic acid
(TCA; 5% v/v final). Samples which received the addition of TCA prior
to the radioisotope served as blanks. The samples were centrifuged at
16000 x g for 7 min and the supernatant was removed. The pellet was
washed once with 5% TCA and once with 80% ethanol. Liquid
scintillation cocktail was added directly to the centrifuge tube which
were then radioassayed.
References
Fuhrman, J. A. and F. Azam 1980. Bacterioplankton secondary production
estimates for coastal waters of British Columbia, Antarctica and
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</pre>
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:Niskin bottles were mounted on the CTD rosette. 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: TT043
TT043
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel
TT043
Michael R. Roman
University of Maryland Center for Environmental Science
http://osprey.bcodmo.org/datasetDeployment.cfm?ddid=2580&did=353&flag=view
Report describing TT043
Cruise: TT045
TT045
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel
TT045
John F. Marra
Lamont-Doherty Earth Observatory
Cruise: TT049
TT049
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel
TT049
Richard Barber
Duke University
Cruise: TT054
TT054
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel
TT054
Wilford D. Gardner
Texas A&M University
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel