Bacterial abundance, thymidine incorporation, bottle casts from R/V Endeavor cruise EN198 in the North Atlantic in 1989 (U.S. JGOFS NABE project)

Website: https://www.bco-dmo.org/dataset/2572
Version: November 28, 2001
Version Date: 2001-11-28

Project
» U.S. JGOFS North Atlantic Bloom Experiment (NABE)

Program
» U.S. Joint Global Ocean Flux Study (U.S. JGOFS)
ContributorsAffiliationRole
Ducklow, Hugh W.Marine Biological Laboratory Ecosystems Center (MBL - Ecosystems)Principal Investigator
Chandler, Cynthia L.Woods Hole Oceanographic Institution (WHOI BCO-DMO)BCO-DMO Data Manager


Dataset Description

Bacterial abundance, thymidine incorporation, bottle casts

Acquisition Description

   PI:              Hugh Ducklow
   of:              Virginia Institute of Marine Science
   dataset:         Bacteria abundance, thymidine incorporation
   dates:           June 30, 1989 to July 04, 1989
   location:        N: 59.535  S: 59.4733  W: -21.0183  E: -20.8217
   project/cruise:  North Atlantic Bloom Experiment/Endeavor 198
   ship:            R/V Endeavor
 
   DMO Note:  Bacteria data from the NABE Atlantis II cruise 
are reported with the biology dataset for that cruise.

Methodology

BACTERIAL ABUNDANCE & BACTERIAL THYMIDINE & LEUCINE INCORPORATION (Ducklow, HPEL)

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.

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 (

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.

US JGOFS NABE Bacterial Data

 
    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:

Abundance:

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.

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 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 (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.

Biomass/production/systhesis rate conversions:
 
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.


References 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. DMO note: The Data Management Office has changed the units of the parameters "bact_het_mic" from cells/liter*10^9 to cells/milliliter

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Parameters

ParameterDescriptionUnits
eventevent number per event log dimensionless
stastation number per event log dimensionless
castcast number, consecutive within station dimensionless
datedate reported as YYYYMMDD YYYYMMDD
timetime reported as HHmm, GMT hours/minutes
latlatitude, minus = south decimal degrees
lonlongitude, minus = west, decimal degrees
depth_nnominal depth of sample meters
thy_incorpthymidine incorporation picomoles/liter/hour
bact_het_origheterotrophic bacteria abundance, original units; microscopy cells/liter *10^9
bact_het_micheterotrophic bacteria abundance, microscopy cells/milliliter


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Instruments

Dataset-specific Instrument Name
Niskin Bottle
Generic Instrument Name
Niskin bottle
Dataset-specific Description
Niskin rosette bottles used to collect thymidine incorporation samples.
Generic 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.


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Deployments

EN198

Website
Platform
R/V Endeavor
Start Date
1989-06-28
End Date
1989-07-07
Description
post bloom cruise; 7 locations; 63°N 25°W to 59°N 14°W

Acquisition Description
PI: Hugh Ducklow of: Virginia Institute of Marine Science dataset: Bacteria abundance, thymidine incorporation dates: June 30, 1989 to July 04, 1989 location: N: 59.535 S: 59.4733 W: -21.0183 E: -20.8217 project/cruise: North Atlantic Bloom Experiment/Endeavor 198 ship: R/V Endeavor Methodology BACTERIAL ABUNDANCE & BACTERIAL THYMIDINE & LEUCINE INCORPORATION (Ducklow, HPEL) 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. 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 ( 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. US JGOFS NABE Bacterial Data 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: Abundance: 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. 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 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 (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. Biomass/production/systhesis rate conversions: 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. References 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. DMO note: The Data Management Office has changed the units of the parameters "bact_het_mic" from cells/liter*10^9 to cells/milliliter


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Project Information

U.S. JGOFS North Atlantic Bloom Experiment (NABE)


Coverage: North Atlantic


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 Atlantis II and R/V Endeavor 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.

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.

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).



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Program Information

U.S. Joint Global Ocean Flux Study (U.S. JGOFS)


Coverage: Global


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).



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Funding

Funding SourceAward
National Science Foundation (NSF)

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