http://lod.bco-dmo.org/id/dataset/4018
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
2013-08-22
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Abundance and biomass of ciliates from inverted microscope counts from samples taken on R/V Atlantic Explorer cruises AE1102, AE1118, AE1206, AE1219 in the Sargasso Sea, Bermuda Atlantic Time-Series Station in 2011-2012 (Trophic BATS project)
2013-08-22
publication
2013-08-22
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2019-08-06
publication
https://doi.org/10.1575/1912/bco-dmo.4018.1
Susanne Neuer
Arizona 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: Neuer, S. (2013) Abundance and biomass of ciliates from inverted microscope counts from samples taken on R/V Atlantic Explorer cruises AE1102, AE1118, AE1206, AE1219 in the Sargasso Sea, Bermuda Atlantic Time-Series Station in 2011-2012 (Trophic BATS project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2013-08-22 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.4018.1 [access date]
Abundance and biomass of ciliates in the Sargasso Sea from inverted microscope counts. Dataset Description: <p>Abundance (cells per L) and biomass (ng C per L) of ciliates from samples collected during four cruises in the Sargasso Sea during spring and summer 2011-2012.</p>
<p>Plot of total_biomass vs. depth. (Generated by BCO-DMO.) Click the image to view a larger version.</p>
<p><a href="http://dmoserv3.bco-dmo.org/data_docs/Trophic_BATS/ciliates_biomass_v_depth.png"><img alt="" src="https://datadocs.bco-dmo.org/d3/data_docs/Trophic_BATS/ciliates_biomass_v_depth.png" style="width:302px" /></a></p> Methods and Sampling: <p><strong>Water Column Sampling:</strong><br />
Water column sampling was performed on four cruises during the spring and the summer of 2011 and 2012 at the Bermuda Atlantic Time-series Study station (31’40°N 64’10°W, BATS) and in the mesoscale eddies found in the surrounding area of the Sargasso Sea. For each cruise, 2 stations were sampled, usually in the center of a mesoscale eddy and at BATS. The edge of the eddy was sample two times, as well. To be able to get a better reproducibility of data, each experiment was replicated.<br />
<br />
For each experiment, seawater samples were collected pre-dawn (on deck 2:30-4:00, local time) at four different depths within the euphotic zone (20m, 50m, 80m and the Deep Chlorophyll Maximum, DCM). Twenty-one 10L Niskin bottles were attached to a rosette with conductivity, temperature, depth sensors (CTD), and an in vivo fluorometer. This sensor allowed for recording in real time of chlorophyll fluorescence and the DCM for each station. The water that was collected from the 10L Niskin bottles was sampled for abundance and biomass of the plankton community.</p>
<p><strong>Microscopy Analyses:</strong><br />
Inverted microscopy was used to determine abundance and biomass of planktonic ciliates. Seawater was collected into 200ml amber glass bottles which had previously been supplied with 2.5% of Lugol’s dye (v/v). Samples were stored in the dark and at room temperature onboard ship and in the laboratory at ASU. 100 ml of sample were settled onto settling chambers for 48hr according to the Utermöhl method (Utermöhl, 1931). A Nikon Elipse TE300 inverted microscope was used at 40x magnification to count the entire slide and all the ciliates found were measured and classified based on the classification system introduced by Agatha (2004) and Agatha &amp; Struder-Kypke (2007). Ciliates were classified into 4 standard shapes: prolate spheroid, sphere, cone, cone + half sphere.</p>
<p>Biomass calculations were done for each category of organism counted. Biovolume for each group was determined based on size and shape of the organism by approximating the closest geometric shape (Hillebrand et al. 1999) and then converted into units of carbon based on the carbon to volume ratio (Menden-Deuer and Lessard 2000). To determine the carbon biomass of the ciliates, carbon to volume conversion factors were used, as in Putt and Stoecker (1989). The 95% confidence intervals were calculated according to Lund et al. (1958).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1030476 Award URL: http://www.nsf.gov/awardsearch/showAward?AWD_ID=1030476&HistoricalAwards=false
completed
Susanne Neuer
Arizona State University
480-727-7254
College of Liberal Arts and Sciences School of Life Sciences 427 East Tyler Mall
Tempe
AZ
85287-4501
USA
susanne.neuer@asu.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
cruise_id
cast
station
location_description
lat
lon
depth
total_biomass
taxon
abundance
abund_upper_95pcnt_CI
abund_lower_95pcnt_CI
biomass
Niskin bottle
Inverted Microscope
theme
None, User defined
cruise id
cast
station
site description
latitude
longitude
depth
biomass carbon
taxon
abundance
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
Niskin bottle
Inverted Microscope
instrument
BCO-DMO Standard Instruments
AE1102
AE1118
AE1206
AE1219
service
Deployment Activity
Sargasso Sea, BATS site
Sargasso Sea; Bermuda Atlantic Time-Series Station; 31 N 64 S
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.
Ocean Carbon and Biogeochemistry
http://us-ocb.org/
Ocean Carbon and Biogeochemistry
The Ocean Carbon and Biogeochemistry (OCB) program focuses on the ocean's role as a component of the global Earth system, bringing together research in geochemistry, ocean physics, and ecology that inform on and advance our understanding of ocean biogeochemistry. The overall program goals are to promote, plan, and coordinate collaborative, multidisciplinary research opportunities within the U.S. research community and with international partners. Important OCB-related activities currently include: the Ocean Carbon and Climate Change (OCCC) and the North American Carbon Program (NACP); U.S. contributions to IMBER, SOLAS, CARBOOCEAN; and numerous U.S. single-investigator and medium-size research projects funded by U.S. federal agencies including NASA, NOAA, and NSF.
The scientific mission of OCB is to study the evolving role of the ocean in the global carbon cycle, in the face of environmental variability and change through studies of marine biogeochemical cycles and associated ecosystems.
The overarching OCB science themes include improved understanding and prediction of: 1) oceanic uptake and release of atmospheric CO2 and other greenhouse gases and 2) environmental sensitivities of biogeochemical cycles, marine ecosystems, and interactions between the two.
The OCB Research Priorities (updated January 2012) include: ocean acidification; terrestrial/coastal carbon fluxes and exchanges; climate sensitivities of and change in ecosystem structure and associated impacts on biogeochemical cycles; mesopelagic ecological and biogeochemical interactions; benthic-pelagic feedbacks on biogeochemical cycles; ocean carbon uptake and storage; and expanding low-oxygen conditions in the coastal and open oceans.
OCB
largerWorkCitation
program
Plankton Community Composition and Trophic Interactions as Modifiers of Carbon Export in the Sargasso Sea
https://www.bco-dmo.org/project/2150
Plankton Community Composition and Trophic Interactions as Modifiers of Carbon Export in the Sargasso Sea
<p>Fluxes of particulate carbon from the surface ocean are greatly influenced by the size, taxonomic composition and trophic interactions of the resident planktonic community. Large and/or heavily-ballasted phytoplankton such as diatoms and coccolithophores are key contributors to carbon export due to their high sinking rates and direct routes of export through large zooplankton. The potential contributions of small, unballasted phytoplankton, through aggregation and/or trophic re-packaging, have been recognized more recently. This recognition comes as direct observations in the field show unexpected trends. In the Sargasso Sea, for example, shallow carbon export has increased in the last decade but the corresponding shift in phytoplankton community composition during this time has not been towards larger cells like diatoms. Instead, the abundance of the picoplanktonic cyanobacterium, Synechococccus, has increased significantly. The trophic pathways that link the increased abundance of Synechococcus to carbon export have not been characterized. These observations helped to frame the overarching research question, "How do plankton size, community composition and trophic interactions modify carbon export from the euphotic zone". Since small phytoplankton are responsible for the majority of primary production in oligotrophic subtropical gyres, the trophic interactions that include them must be characterized in order to achieve a mechanistic understanding of the function of the biological pump in the oligotrophic regions of the ocean.</p>
<p>This requires a complete characterization of the major organisms and their rates of production and consumption. Accordingly, the research objectives are: 1) to characterize (qualitatively and quantitatively) trophic interactions between major plankton groups in the euphotic zone and rates of, and contributors to, carbon export and 2) to develop a constrained food web model, based on these data, that will allow us to better understand current and predict near-future patterns in export production in the Sargasso Sea.</p>
<p>The investigators will use a combination of field-based process studies and food web modeling to quantify rates of carbon exchange between key components of the ecosystem at the Bermuda Atlantic Time-series Study (BATS) site. Measurements will include a novel DNA-based approach to characterizing and quantifying planktonic contributors to carbon export. The well-documented seasonal variability at BATS and the occurrence of mesoscale eddies will be used as a natural laboratory in which to study ecosystems of different structure. This study is unique in that it aims to characterize multiple food web interactions and carbon export simultaneously and over similar time and space scales. A key strength of the proposed research is also the tight connection and feedback between the data collection and modeling components.</p>
<p>Characterizing the complex interactions between the biological community and export production is critical for predicting changes in phytoplankton species dominance, trophic relationships and export production that might occur under scenarios of climate-related changes in ocean circulation and mixing. The results from this research may also contribute to understanding of the biological mechanisms that drive current regional to basin scale variability in carbon export in oligotrophic gyres.</p>
Trophic BATS
largerWorkCitation
project
eng; USA
oceans
Sargasso Sea, BATS site; Sargasso Sea; Bermuda Atlantic Time-Series Station; 31 N 64 S
-64.83
-64.17
30.83
33.48
2011-02-23
2012-07-31
Sargasso Sea, BATS site
0
BCO-DMO catalogue of parameters from Abundance and biomass of ciliates from inverted microscope counts from samples taken on R/V Atlantic Explorer cruises AE1102, AE1118, AE1206, AE1219 in the Sargasso Sea, Bermuda Atlantic Time-Series Station in 2011-2012 (Trophic BATS 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/36050.rdf
Name: cruise_id
Units: dimensionless
Description: Official cruise identifier e.g. AE1102 = R/V Atlantic Explorer cruise number 1102.
http://lod.bco-dmo.org/id/dataset-parameter/36051.rdf
Name: cast
Units: dimensionless
Description: Cast number.
http://lod.bco-dmo.org/id/dataset-parameter/36052.rdf
Name: station
Units: dimensionless
Description: Station number.
http://lod.bco-dmo.org/id/dataset-parameter/36053.rdf
Name: location_description
Units: dimensionless
Description: Description of sampling location.
http://lod.bco-dmo.org/id/dataset-parameter/36054.rdf
Name: lat
Units: decimal degrees
Description: Latitude. Positive values = North.
http://lod.bco-dmo.org/id/dataset-parameter/36055.rdf
Name: lon
Units: decimal degrees
Description: Longitude. Positive values = East.
http://lod.bco-dmo.org/id/dataset-parameter/36056.rdf
Name: depth
Units: meters
Description: Sample depth.
http://lod.bco-dmo.org/id/dataset-parameter/36057.rdf
Name: total_biomass
Units: nanograms C per Liter
Description: Total biomass (ng C/L) at the particular cast and depth.
http://lod.bco-dmo.org/id/dataset-parameter/36058.rdf
Name: taxon
Units: dimensionless
Description: Name of the taxonomic group.
http://lod.bco-dmo.org/id/dataset-parameter/36059.rdf
Name: abundance
Units: cells per Liter
Description: Abundance of planktonic ciliates (cells/L).
http://lod.bco-dmo.org/id/dataset-parameter/36060.rdf
Name: abund_upper_95pcnt_CI
Units: cells per Liter
Description: Upper 95% confidence interval for abundance.
http://lod.bco-dmo.org/id/dataset-parameter/36061.rdf
Name: abund_lower_95pcnt_CI
Units: cells per Liter
Description: Lower 95% confidence interval for abundance.
http://lod.bco-dmo.org/id/dataset-parameter/36062.rdf
Name: biomass
Units: nanograms C per Liter
Description: Biomass (ng C/L) of planktonic ciliates.
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
31120
https://darchive.mblwhoilibrary.org/bitstream/1912/24424/1/dataset-4018_ciliate-abundance-and-biomass__v1.tsv
download
https://doi.org/10.1575/1912/bco-dmo.4018.1
download
onLine
dataset
<p><strong>Water Column Sampling:</strong><br />
Water column sampling was performed on four cruises during the spring and the summer of 2011 and 2012 at the Bermuda Atlantic Time-series Study station (31’40°N 64’10°W, BATS) and in the mesoscale eddies found in the surrounding area of the Sargasso Sea. For each cruise, 2 stations were sampled, usually in the center of a mesoscale eddy and at BATS. The edge of the eddy was sample two times, as well. To be able to get a better reproducibility of data, each experiment was replicated.<br />
<br />
For each experiment, seawater samples were collected pre-dawn (on deck 2:30-4:00, local time) at four different depths within the euphotic zone (20m, 50m, 80m and the Deep Chlorophyll Maximum, DCM). Twenty-one 10L Niskin bottles were attached to a rosette with conductivity, temperature, depth sensors (CTD), and an in vivo fluorometer. This sensor allowed for recording in real time of chlorophyll fluorescence and the DCM for each station. The water that was collected from the 10L Niskin bottles was sampled for abundance and biomass of the plankton community.</p>
<p><strong>Microscopy Analyses:</strong><br />
Inverted microscopy was used to determine abundance and biomass of planktonic ciliates. Seawater was collected into 200ml amber glass bottles which had previously been supplied with 2.5% of Lugol’s dye (v/v). Samples were stored in the dark and at room temperature onboard ship and in the laboratory at ASU. 100 ml of sample were settled onto settling chambers for 48hr according to the Utermöhl method (Utermöhl, 1931). A Nikon Elipse TE300 inverted microscope was used at 40x magnification to count the entire slide and all the ciliates found were measured and classified based on the classification system introduced by Agatha (2004) and Agatha &amp; Struder-Kypke (2007). Ciliates were classified into 4 standard shapes: prolate spheroid, sphere, cone, cone + half sphere.</p>
<p>Biomass calculations were done for each category of organism counted. Biovolume for each group was determined based on size and shape of the organism by approximating the closest geometric shape (Hillebrand et al. 1999) and then converted into units of carbon based on the carbon to volume ratio (Menden-Deuer and Lessard 2000). To determine the carbon biomass of the ciliates, carbon to volume conversion factors were used, as in Putt and Stoecker (1989). The 95% confidence intervals were calculated according to Lund et al. (1958).</p>
Specified by the Principal Investigator(s)
<p>BCO-DMO Processing Notes:<br />
- Moved cruise_id, location_description, station, and cast into columns.<br />
- Replaced blanks with 'nd' to indicate 'no data'.<br />
- Removed 'm' from the depth column.<br />
- Replaced "Tot#/L" with "Total_num_per_liter" in the taxon column.<br />
- Added lat and lon for each station &amp; cast from the metadata form.</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:Samples were collected using 10-Liter Niskin bottles attached to a 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/
Inverted Microscope
Inverted Microscope
PI Supplied Instrument Name: Inverted Microscope PI Supplied Instrument Description:Ciliate abundance and biomass was determined using bright-field inverted microscopy (Amacher et al. 2009; Neuer and Cowles 1994). A Nikon Elipse TE300 inverted microscope was used at 40x magnification to count the entire slide. Instrument Name: Inverted Microscope Instrument Short Name: Instrument Description: An inverted microscope is a microscope with its light source and condenser on the top, above the stage pointing down, while the objectives and turret are below the stage pointing up. It was invented in 1850 by J. Lawrence Smith, a faculty member of Tulane University (then named the Medical College of Louisiana).
Inverted microscopes are useful for observing living cells or organisms at the bottom of a large container (e.g. a tissue culture flask) under more natural conditions than on a glass slide, as is the case with a conventional microscope. Inverted microscopes are also used in micromanipulation applications where space above the specimen is required for manipulator mechanisms and the microtools they hold, and in metallurgical applications where polished samples can be placed on top of the stage and viewed from underneath using reflecting objectives.
The stage on an inverted microscope is usually fixed, and focus is adjusted by moving the objective lens along a vertical axis to bring it closer to or further from the specimen. The focus mechanism typically has a dual concentric knob for coarse and fine adjustment. Depending on the size of the microscope, four to six objective lenses of different magnifications may be fitted to a rotating turret known as a nosepiece. These microscopes may also be fitted with accessories for fitting still and video cameras, fluorescence illumination, confocal scanning and many other applications. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB05/
Cruise: AE1102
AE1102
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel
AE1102
Tammi Richardson
University of South Carolina
Cruise: AE1118
AE1118
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel
AE1118
Tammi Richardson
University of South Carolina
Cruise: AE1206
AE1206
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel
AE1206
Tammi Richardson
University of South Carolina
Cruise: AE1219
AE1219
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel
AE1219
Tammi Richardson
University of South Carolina
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel