http://lod.bco-dmo.org/id/dataset/2572
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
2010-06-16
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Bacterial abundance, thymidine incorporation, bottle casts from R/V Endeavor cruise EN198 in the North Atlantic in 1989 (U.S. JGOFS NABE project)
2001-11-28
publication
2001-11-28
revision
BCO-DMO Linked Data URI
2001-11-28
creation
http://lod.bco-dmo.org/id/dataset/2572
Hugh W. Ducklow
Marine Biological Laboratory Ecosystems Center
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: Ducklow, H. W. (2001) Bacterial abundance, thymidine incorporation, bottle casts from R/V Endeavor cruise EN198 in the North Atlantic in 1989 (U.S. JGOFS NABE project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version November 28, 2001) Version Date 2001-11-28 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/2572 [access date]
Bacterial abundance, thymidine incorporation, bottle casts Methods and Sampling: <pre>
<b>PI:</b> Hugh Ducklow
<b>of:</b> Virginia Institute of Marine Science
<b>dataset:</b> Bacteria abundance, thymidine incorporation
<b>dates:</b> June 30, 1989 to July 04, 1989
<b>location:</b> N: 59.535 S: 59.4733 W: -21.0183 E: -20.8217
<b>project/cruise:</b> North Atlantic Bloom Experiment/Endeavor 198
<b>ship:</b> R/V Endeavor
<b>DMO Note: </b> Bacteria data from the NABE Atlantis II cruise <br />
are reported with the biology dataset for that cruise.</h2>
<h2>Methodology</h2>
<h3>BACTERIAL ABUNDANCE & BACTERIAL THYMIDINE
& LEUCINE INCORPORATION (Ducklow, HPEL)</h3>
Abundance samples preserved in 1.25% glutaraldehyde and stored at 5�
C until microscopy was performed at Horn Point Environmental Laboratory.
All samples were enumerated according to the Acridine Orange Direct Count
technique of Hobbie et al., (1977) with modifications by Helen Quinby.
Samples were enumerated on a Nikon Optiphot epifluorescence microscope
at 1850x with a 100 watt Mercury lamp.
<p> Thymidine incorporation samples collected from Niskin rosette casts
were immediately processed as described in Ducklow and Hill (1985),
with the following modifications: Samples were incubated with 5 nM 3H-thymidine
(New England Nuclear, sp. act. 81 Ci/mmol) in polycarbonate bottles,
disposable polyproplyene centrifuge tubes or Whirl-Pak bags. Incubations
were terminated with addition of 0.37% formaldehyde, then filtered onto
0.2 �m Nuclepore filters. Extractions were carried out by rinsing
each filter on its funnel support 3 times with 5% ice cold TCA, over
a weak vacuum (<10 in. Hg), then 3 times with 80% ice cold ethanol.
All extracted filters were stored dry in scintillation vials for counting
at Horn Point Environmental Laboratory.
</p><p> Leucine incorporation samples were treated according to the method
described in Kirchman et al., (1985), with the following modifications:
Samples were incubated with 0.5 nM 3H- leucine (NEN; Sp. Act. 73 Ci/mmol)
and 10 nM nonradioactive leucine, then treated as described for thymidine.
</pre>
<h3>US JGOFS NABE Bacterial Data</h3>
<pre>
Bacterial data were collected on the US JGOFS NABE cruises aboard RV
ATLANTIS II legs 2 and 3 and Endeavor cruise 198 by Hugh Ducklow, David
Kirchman, Helen Quinby and Hans Dam. On cruise 2, only bacterial abundance
was measured. On cruise 3, bacterial abundance, and bacterial thymidine and
leucine incorporation were measured. On Endeavor cruise 198 only bacteria
abundance and thymidine incorporation were measured by the following methods:
<b>Abundance:</b>
Samples preserved in 1.25% glutaraldehyde and stored at 5C until microscopy was
performed at Horn Point. All samples were enumerated according to the Acridine
Orange Direct Count technique of Hobbie et al., (1977) with modifications by
Helen Quinby. Samples were enumerated on a Nikon Optiphot epifluorescence
microscope at 1850X with a 100 watt Mercury lamp.
<b>Thymidine Incorporation:</b>
Samples collected from Niskin rosette casts were immediately processed as
described in Ducklow and Hill (1985), with the following modifications:
Samples were incubated with 5 nM 3H-thymidine (New England Nuclear, sp. act. 81
Ci/mmol) in polycarbonate bottles, disposable polyproplyene centrifuge tubes or
Whirl-Pak bags. Incubations were terminated with addition of 0.37%
formaldehyde, then filtered onto 0.2 um Nuclepore filters. Extractions were
carried out by rinsing each filter on its funnel support 3 times with 5% ice
cold TCA, over a weak vacuum (< 10 in. Hg), then 3 times with 80% ice cold
ethanol. All extracted filters were stored dry in scintillation vials for
counting at Horn Point.
Additional samples were treated to purify the labelled DNA following the method
of Wicks et al., (1987). 95% of the label in the cold TCA extracts was in pure
DNA. (Data available from HWD).
<b>Leucine Incorporation:</b>
Samples were treated according to the method described in Kirchman et al.,
(1985), with the following modifications:
Samples were incubated with 0.5 nM 3H-leucine (NEN; Sp. Act. 73 Ci/mmol) and 10
nM nonradioactive leucine, then treated as described for thymidine.
<b>Biomass/production/systhesis rate conversions:</b>
The bacteria abundance data can be converted into bacterial biomass (ugC or ugN l-1)
as described for example in Lee and Fuhrman (1988). We will be measuring cell
biovolumes for this conversion and have not supplied nominal biomass data at
this time.
The THYINCORP data can be converted into bacterial production rates (ugC or ugN
l-1 hr-1) as discussed in Ducklow and Hill (1985). We performed separate
experiments to determine the conversion factors, and will report the data
separately. The THYINCORP data provide a relative index of differences in
bacterial production in space and time. Data on the biovolume and rate
conversion factors are required for translation into absolute units.
The LEUINCORP data can be converted into bacterial protein synthesis rates (ugC
or ugN l-1 hr-1) as discussed in Chin-Leo and Kirchman, (1988). We performed
separate experiments to determine the conversion factors, and will report the
data separately. The LEUINCORP data provide a relative index of differences in
protein synthesis in space and time. Data on the biovolume and rate conversion
factors are required for translation into absolute units.
<hr>
<b>References</b>
Chin-Leo, G. And D.L. Kirchman. 1988. Estimating bacterial production in
natural waters from the simultaneous incorporation of thymidine and
leucine. Appl. Environ. Microbiol. 54:1934-39.
Ducklow, H.W., and S.M. Hill. 1985b. Tritiated thymidine incorporation and the
growth of heterotrophic bacteria in warm core rings. Limnol. Oceanogr.
30:260-272.
Hobbie, J.E., R.J. Daley, and S. Jasper. 1977. Use of Nuclepore filters for
counting bacteria by fluorescence 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 waters.
Appl. Environ. Microbiol. 49: 599-607.
Lee, S. and J.A. Fuhrman. 1987. Relationships between biovolume and biomass of
naturally-derived marine bacterioplankton. Appl. Environ. Microbiol.
52:1298-1303.
Wicks, R.J. and R.D.Robarts, 1987, The extraction and purification of DNA
labelled with methyl-3H-thymidine in aquatic bacterial production studies,
J. Plankton Res. 9:1159-66.
<b>DMO note:</b>
The Data Management Office has changed the units of the parameters
"bact_het_mic" from cells/liter*10^9 to cells/milliliter
</pre>
Funding provided by National Science Foundation (NSF) Award Number: unknown NABE NSF
completed
Hugh W. Ducklow
Marine Biological Laboratory Ecosystems Center
508 289-7193
LDEO
Palisades
NY
10964
USA
hducklow@ldeo.columbia.edu
pointOfContact
asNeeded
Dataset Version: November 28, 2001
Unknown
event
sta
cast
date
time
lat
lon
depth_n
thy_incorp
bact_het_orig
bact_het_mic
Niskin Bottle
theme
None, User defined
event
station number
cast
date
time of day
latitude
longitude
depth nominal
thymidine incorporation rate
heterotrophic bacteria abundance
heterotrophic bacteria abundance
featureType
BCO-DMO Standard Parameters
Niskin bottle
instrument
BCO-DMO Standard Instruments
EN198
service
Deployment Activity
U.S. JGOFS North Atlantic
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 North Atlantic Bloom Experiment
http://usjgofs.whoi.edu/research/nabe.html
U.S. JGOFS North Atlantic Bloom Experiment
<p>One of the first major activities of JGOFS was a multinational pilot project, North Atlantic Bloom Experiment (NABE), carried out along longitude 20° West in 1989 through 1991. The United States participated in 1989 only, with the April deployment of two sediment trap arrays at 48° and 34° North. Three process-oriented cruises where conducted, April through July 1989, from R/V <em>Atlantis II</em> and R/V <em>Endeavor</em> focusing on sites at 46° and 59° North. Coordination of the NABE process-study cruises was supported by NSF-OCE award # 8814229. Ancillary sea surface mapping and AXBT profiling data were collected from NASA's P3 aircraft for a series of one day flights, April through June 1989.</p>
<p>A detailed description of NABE and the initial synthesis of the complete program data collection efforts appear in: Topical Studies in Oceanography, JGOFS: The North Atlantic Bloom Experiment (1993), Deep-Sea Research II, Volume 40 No. 1/2.</p>
<p>The U.S. JGOFS Data management office compiled a preliminary NABE data report of U.S. activities: Slagle, R. and G. Heimerdinger, 1991. U.S. Joint Global Ocean Flux Study, North Atlantic Bloom Experiment, Process Study Data Report P-1, April-July 1989. NODC/U.S. JGOFS Data Management Office, Woods Hole Oceanographic Institution, 315 pp. (out of print).</p>
NABE
largerWorkCitation
project
eng; USA
oceans
U.S. JGOFS North Atlantic
2001-11-28
North Atlantic
0
BCO-DMO catalogue of parameters from Bacterial abundance, thymidine incorporation, bottle casts from R/V Endeavor cruise EN198 in the North Atlantic in 1989 (U.S. JGOFS NABE 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/10834.rdf
Name: event
Units: dimensionless
Description: <p>event number per event log</p>
http://lod.bco-dmo.org/id/dataset-parameter/10835.rdf
Name: sta
Units: dimensionless
Description: <p>station number per event log</p>
http://lod.bco-dmo.org/id/dataset-parameter/10836.rdf
Name: cast
Units: dimensionless
Description: <p>cast number, consecutive within station</p>
http://lod.bco-dmo.org/id/dataset-parameter/10837.rdf
Name: date
Units: YYYYMMDD
Description: <p>date reported as YYYYMMDD</p>
http://lod.bco-dmo.org/id/dataset-parameter/10838.rdf
Name: time
Units: hours/minutes
Description: <p>time reported as HHmm, GMT</p>
http://lod.bco-dmo.org/id/dataset-parameter/10839.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude, minus = south</p>
http://lod.bco-dmo.org/id/dataset-parameter/10840.rdf
Name: lon
Units: decimal degrees
Description: <p>longitude, minus = west,</p>
http://lod.bco-dmo.org/id/dataset-parameter/10841.rdf
Name: depth_n
Units: meters
Description: <p>nominal depth of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/10842.rdf
Name: thy_incorp
Units: picomoles/liter/hour
Description: <p>thymidine incorporation</p>
http://lod.bco-dmo.org/id/dataset-parameter/10843.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/10844.rdf
Name: bact_het_mic
Units: cells/milliliter
Description: <p>heterotrophic bacteria abundance, microscopy</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
2409
https://datadocs.bco-dmo.org/file/6YYMwqgcVDEvlK/bacteria.csv
bacteria.csv
Primary data file for dataset ID 2572
download
https://osprey.bco-dmo.org/dataset/2572/data/download
download
onLine
dataset
<pre>
<b>PI:</b> Hugh Ducklow
<b>of:</b> Virginia Institute of Marine Science
<b>dataset:</b> Bacteria abundance, thymidine incorporation
<b>dates:</b> June 30, 1989 to July 04, 1989
<b>location:</b> N: 59.535 S: 59.4733 W: -21.0183 E: -20.8217
<b>project/cruise:</b> North Atlantic Bloom Experiment/Endeavor 198
<b>ship:</b> R/V Endeavor
<b>DMO Note: </b> Bacteria data from the NABE Atlantis II cruise <br />
are reported with the biology dataset for that cruise.</h2>
<h2>Methodology</h2>
<h3>BACTERIAL ABUNDANCE & BACTERIAL THYMIDINE
& LEUCINE INCORPORATION (Ducklow, HPEL)</h3>
Abundance samples preserved in 1.25% glutaraldehyde and stored at 5�
C until microscopy was performed at Horn Point Environmental Laboratory.
All samples were enumerated according to the Acridine Orange Direct Count
technique of Hobbie et al., (1977) with modifications by Helen Quinby.
Samples were enumerated on a Nikon Optiphot epifluorescence microscope
at 1850x with a 100 watt Mercury lamp.
<p> Thymidine incorporation samples collected from Niskin rosette casts
were immediately processed as described in Ducklow and Hill (1985),
with the following modifications: Samples were incubated with 5 nM 3H-thymidine
(New England Nuclear, sp. act. 81 Ci/mmol) in polycarbonate bottles,
disposable polyproplyene centrifuge tubes or Whirl-Pak bags. Incubations
were terminated with addition of 0.37% formaldehyde, then filtered onto
0.2 �m Nuclepore filters. Extractions were carried out by rinsing
each filter on its funnel support 3 times with 5% ice cold TCA, over
a weak vacuum (<10 in. Hg), then 3 times with 80% ice cold ethanol.
All extracted filters were stored dry in scintillation vials for counting
at Horn Point Environmental Laboratory.
</p><p> Leucine incorporation samples were treated according to the method
described in Kirchman et al., (1985), with the following modifications:
Samples were incubated with 0.5 nM 3H- leucine (NEN; Sp. Act. 73 Ci/mmol)
and 10 nM nonradioactive leucine, then treated as described for thymidine.
</pre>
<h3>US JGOFS NABE Bacterial Data</h3>
<pre>
Bacterial data were collected on the US JGOFS NABE cruises aboard RV
ATLANTIS II legs 2 and 3 and Endeavor cruise 198 by Hugh Ducklow, David
Kirchman, Helen Quinby and Hans Dam. On cruise 2, only bacterial abundance
was measured. On cruise 3, bacterial abundance, and bacterial thymidine and
leucine incorporation were measured. On Endeavor cruise 198 only bacteria
abundance and thymidine incorporation were measured by the following methods:
<b>Abundance:</b>
Samples preserved in 1.25% glutaraldehyde and stored at 5C until microscopy was
performed at Horn Point. All samples were enumerated according to the Acridine
Orange Direct Count technique of Hobbie et al., (1977) with modifications by
Helen Quinby. Samples were enumerated on a Nikon Optiphot epifluorescence
microscope at 1850X with a 100 watt Mercury lamp.
<b>Thymidine Incorporation:</b>
Samples collected from Niskin rosette casts were immediately processed as
described in Ducklow and Hill (1985), with the following modifications:
Samples were incubated with 5 nM 3H-thymidine (New England Nuclear, sp. act. 81
Ci/mmol) in polycarbonate bottles, disposable polyproplyene centrifuge tubes or
Whirl-Pak bags. Incubations were terminated with addition of 0.37%
formaldehyde, then filtered onto 0.2 um Nuclepore filters. Extractions were
carried out by rinsing each filter on its funnel support 3 times with 5% ice
cold TCA, over a weak vacuum (< 10 in. Hg), then 3 times with 80% ice cold
ethanol. All extracted filters were stored dry in scintillation vials for
counting at Horn Point.
Additional samples were treated to purify the labelled DNA following the method
of Wicks et al., (1987). 95% of the label in the cold TCA extracts was in pure
DNA. (Data available from HWD).
<b>Leucine Incorporation:</b>
Samples were treated according to the method described in Kirchman et al.,
(1985), with the following modifications:
Samples were incubated with 0.5 nM 3H-leucine (NEN; Sp. Act. 73 Ci/mmol) and 10
nM nonradioactive leucine, then treated as described for thymidine.
<b>Biomass/production/systhesis rate conversions:</b>
The bacteria abundance data can be converted into bacterial biomass (ugC or ugN l-1)
as described for example in Lee and Fuhrman (1988). We will be measuring cell
biovolumes for this conversion and have not supplied nominal biomass data at
this time.
The THYINCORP data can be converted into bacterial production rates (ugC or ugN
l-1 hr-1) as discussed in Ducklow and Hill (1985). We performed separate
experiments to determine the conversion factors, and will report the data
separately. The THYINCORP data provide a relative index of differences in
bacterial production in space and time. Data on the biovolume and rate
conversion factors are required for translation into absolute units.
The LEUINCORP data can be converted into bacterial protein synthesis rates (ugC
or ugN l-1 hr-1) as discussed in Chin-Leo and Kirchman, (1988). We performed
separate experiments to determine the conversion factors, and will report the
data separately. The LEUINCORP data provide a relative index of differences in
protein synthesis in space and time. Data on the biovolume and rate conversion
factors are required for translation into absolute units.
<hr>
<b>References</b>
Chin-Leo, G. And D.L. Kirchman. 1988. Estimating bacterial production in
natural waters from the simultaneous incorporation of thymidine and
leucine. Appl. Environ. Microbiol. 54:1934-39.
Ducklow, H.W., and S.M. Hill. 1985b. Tritiated thymidine incorporation and the
growth of heterotrophic bacteria in warm core rings. Limnol. Oceanogr.
30:260-272.
Hobbie, J.E., R.J. Daley, and S. Jasper. 1977. Use of Nuclepore filters for
counting bacteria by fluorescence 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 waters.
Appl. Environ. Microbiol. 49: 599-607.
Lee, S. and J.A. Fuhrman. 1987. Relationships between biovolume and biomass of
naturally-derived marine bacterioplankton. Appl. Environ. Microbiol.
52:1298-1303.
Wicks, R.J. and R.D.Robarts, 1987, The extraction and purification of DNA
labelled with methyl-3H-thymidine in aquatic bacterial production studies,
J. Plankton Res. 9:1159-66.
<b>DMO note:</b>
The Data Management Office has changed the units of the parameters
"bact_het_mic" from cells/liter*10^9 to cells/milliliter
</pre>
from Cruise: EN198 <pre>
<b>PI:</b> Hugh Ducklow
<b>of:</b> Virginia Institute of Marine Science
<b>dataset:</b> Bacteria abundance, thymidine incorporation
<b>dates:</b> June 30, 1989 to July 04, 1989
<b>location:</b> N: 59.535 S: 59.4733 W: -21.0183 E: -20.8217
<b>project/cruise:</b> North Atlantic Bloom Experiment/Endeavor 198
<b>ship:</b> R/V Endeavor
<h2>Methodology</h2>
<h3>BACTERIAL ABUNDANCE & BACTERIAL THYMIDINE
& LEUCINE INCORPORATION (Ducklow, HPEL)</h3>
Abundance samples preserved in 1.25% glutaraldehyde and stored at 5�
C until microscopy was performed at Horn Point Environmental Laboratory.
All samples were enumerated according to the Acridine Orange Direct Count
technique of Hobbie et al., (1977) with modifications by Helen Quinby.
Samples were enumerated on a Nikon Optiphot epifluorescence microscope
at 1850x with a 100 watt Mercury lamp.
<p> Thymidine incorporation samples collected from Niskin rosette casts
were immediately processed as described in Ducklow and Hill (1985),
with the following modifications: Samples were incubated with 5 nM 3H-thymidine
(New England Nuclear, sp. act. 81 Ci/mmol) in polycarbonate bottles,
disposable polyproplyene centrifuge tubes or Whirl-Pak bags. Incubations
were terminated with addition of 0.37% formaldehyde, then filtered onto
0.2 �m Nuclepore filters. Extractions were carried out by rinsing
each filter on its funnel support 3 times with 5% ice cold TCA, over
a weak vacuum (<10 in. Hg), then 3 times with 80% ice cold ethanol.
All extracted filters were stored dry in scintillation vials for counting
at Horn Point Environmental Laboratory.
</p><p> Leucine incorporation samples were treated according to the method
described in Kirchman et al., (1985), with the following modifications:
Samples were incubated with 0.5 nM 3H- leucine (NEN; Sp. Act. 73 Ci/mmol)
and 10 nM nonradioactive leucine, then treated as described for thymidine.
</pre>
<h3>US JGOFS NABE Bacterial Data</h3>
<pre>
Bacterial data were collected on the US JGOFS NABE cruises aboard RV
ATLANTIS II legs 2 and 3 and Endeavor cruise 198 by Hugh Ducklow, David
Kirchman, Helen Quinby and Hans Dam. On cruise 2, only bacterial abundance
was measured. On cruise 3, bacterial abundance, and bacterial thymidine and
leucine incorporation were measured. On Endeavor cruise 198 only bacteria
abundance and thymidine incorporation were measured by the following methods:
<b>Abundance:</b>
Samples preserved in 1.25% glutaraldehyde and stored at 5C until microscopy was
performed at Horn Point. All samples were enumerated according to the Acridine
Orange Direct Count technique of Hobbie et al., (1977) with modifications by
Helen Quinby. Samples were enumerated on a Nikon Optiphot epifluorescence
microscope at 1850X with a 100 watt Mercury lamp.
<b>Thymidine Incorporation:</b>
Samples collected from Niskin rosette casts were immediately processed as
described in Ducklow and Hill (1985), with the following modifications:
Samples were incubated with 5 nM 3H-thymidine (New England Nuclear, sp. act. 81
Ci/mmol) in polycarbonate bottles, disposable polyproplyene centrifuge tubes or
Whirl-Pak bags. Incubations were terminated with addition of 0.37%
formaldehyde, then filtered onto 0.2 um Nuclepore filters. Extractions were
carried out by rinsing each filter on its funnel support 3 times with 5% ice
cold TCA, over a weak vacuum (< 10 in. Hg), then 3 times with 80% ice cold
ethanol. All extracted filters were stored dry in scintillation vials for
counting at Horn Point.
Additional samples were treated to purify the labelled DNA following the method
of Wicks et al., (1987). 95% of the label in the cold TCA extracts was in pure
DNA. (Data available from HWD).
<b>Leucine Incorporation:</b>
Samples were treated according to the method described in Kirchman et al.,
(1985), with the following modifications:
Samples were incubated with 0.5 nM 3H-leucine (NEN; Sp. Act. 73 Ci/mmol) and 10
nM nonradioactive leucine, then treated as described for thymidine.
<b>Biomass/production/systhesis rate conversions:</b>
The bacteria abundance data can be converted into bacterial biomass (ugC or ugN l-1)
as described for example in Lee and Fuhrman (1988). We will be measuring cell
biovolumes for this conversion and have not supplied nominal biomass data at
this time.
The THYINCORP data can be converted into bacterial production rates (ugC or ugN
l-1 hr-1) as discussed in Ducklow and Hill (1985). We performed separate
experiments to determine the conversion factors, and will report the data
separately. The THYINCORP data provide a relative index of differences in
bacterial production in space and time. Data on the biovolume and rate
conversion factors are required for translation into absolute units.
The LEUINCORP data can be converted into bacterial protein synthesis rates (ugC
or ugN l-1 hr-1) as discussed in Chin-Leo and Kirchman, (1988). We performed
separate experiments to determine the conversion factors, and will report the
data separately. The LEUINCORP data provide a relative index of differences in
protein synthesis in space and time. Data on the biovolume and rate conversion
factors are required for translation into absolute units.
<hr>
<b>References</b>
Chin-Leo, G. And D.L. Kirchman. 1988. Estimating bacterial production in
natural waters from the simultaneous incorporation of thymidine and
leucine. Appl. Environ. Microbiol. 54:1934-39.
Ducklow, H.W., and S.M. Hill. 1985b. Tritiated thymidine incorporation and the
growth of heterotrophic bacteria in warm core rings. Limnol. Oceanogr.
30:260-272.
Hobbie, J.E., R.J. Daley, and S. Jasper. 1977. Use of Nuclepore filters for
counting bacteria by fluorescence 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 waters.
Appl. Environ. Microbiol. 49: 599-607.
Lee, S. and J.A. Fuhrman. 1987. Relationships between biovolume and biomass of
naturally-derived marine bacterioplankton. Appl. Environ. Microbiol.
52:1298-1303.
Wicks, R.J. and R.D.Robarts, 1987, The extraction and purification of DNA
labelled with methyl-3H-thymidine in aquatic bacterial production studies,
J. Plankton Res. 9:1159-66.
<b>DMO note:</b>
The Data Management Office has changed the units of the parameters
"bact_het_mic" from cells/liter*10^9 to cells/milliliter
</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 rosette bottles used to collect thymidine incorporation samples. 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: EN198
EN198
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel
EN198
William Broenkow
Moss Landing Marine Laboratories
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel