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Title Sum-
Institution Dataset ID
     data   graph     files  public 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)
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The Dataset's Variables and Attributes

Row Type Variable Name Attribute Name Data Type Value
attribute NC_GLOBAL access_formats String .htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson
attribute NC_GLOBAL acquisition_description String Water Column Sampling:
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\u201940\u00b0N 64\u201910\u00b0W, 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.

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.

Microscopy Analyses:
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\u2019s 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 Uterm\u00f6hl method (Uterm\u00f6hl, 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 & Struder-
Kypke (2007). Ciliates were classified into 4 standard shapes: prolate
spheroid, sphere, cone, cone + half sphere.

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).
attribute NC_GLOBAL awards_0_award_nid String 55163
attribute NC_GLOBAL awards_0_award_number String OCE-1030476
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward?AWD_ID=1030476&HistoricalAwards=false (external link)
attribute NC_GLOBAL awards_0_funder_name String NSF Division of Ocean Sciences
attribute NC_GLOBAL awards_0_funding_acronym String NSF OCE
attribute NC_GLOBAL awards_0_funding_source_nid String 355
attribute NC_GLOBAL awards_0_program_manager String David L. Garrison
attribute NC_GLOBAL awards_0_program_manager_nid String 50534
attribute NC_GLOBAL cdm_data_type String Other
attribute NC_GLOBAL comment String Abundance and biomass of ciliates
based on inverted microscope counts
PI: Susanne Neuer (Arizona State U.)
Version: 22 Aug 2013
attribute NC_GLOBAL Conventions String COARDS, CF-1.6, ACDD-1.3
attribute NC_GLOBAL creator_email String info at bco-dmo.org
attribute NC_GLOBAL creator_name String BCO-DMO
attribute NC_GLOBAL creator_type String institution
attribute NC_GLOBAL creator_url String https://www.bco-dmo.org/ (external link)
attribute NC_GLOBAL data_source String extract_data_as_tsv version 2.3 19 Dec 2019
attribute NC_GLOBAL date_created String 2013-08-22T15:43:29Z
attribute NC_GLOBAL date_modified String 2019-08-05T18:55:51Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.4018.1
attribute NC_GLOBAL Easternmost_Easting double -64.17
attribute NC_GLOBAL geospatial_lat_max double 33.48
attribute NC_GLOBAL geospatial_lat_min double 30.83
attribute NC_GLOBAL geospatial_lat_units String degrees_north
attribute NC_GLOBAL geospatial_lon_max double -64.17
attribute NC_GLOBAL geospatial_lon_min double -64.83
attribute NC_GLOBAL geospatial_lon_units String degrees_east
attribute NC_GLOBAL geospatial_vertical_max double 100.0
attribute NC_GLOBAL geospatial_vertical_min double 20.0
attribute NC_GLOBAL geospatial_vertical_positive String down
attribute NC_GLOBAL geospatial_vertical_units String m
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/4018 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_acronym String Niskin bottle
attribute NC_GLOBAL instruments_0_dataset_instrument_description String Samples were collected using 10-Liter Niskin bottles attached to a CTD rosette.
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 6242
attribute NC_GLOBAL instruments_0_description String 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.
attribute NC_GLOBAL instruments_0_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/ (external link)
attribute NC_GLOBAL instruments_0_instrument_name String Niskin bottle
attribute NC_GLOBAL instruments_0_instrument_nid String 413
attribute NC_GLOBAL instruments_0_supplied_name String Niskin bottle
attribute NC_GLOBAL instruments_1_acronym String Inverted Microscope
attribute NC_GLOBAL instruments_1_dataset_instrument_description String 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.
attribute NC_GLOBAL instruments_1_dataset_instrument_nid String 6243
attribute NC_GLOBAL instruments_1_description String 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.
attribute NC_GLOBAL instruments_1_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/LAB05/ (external link)
attribute NC_GLOBAL instruments_1_instrument_name String Inverted Microscope
attribute NC_GLOBAL instruments_1_instrument_nid String 675
attribute NC_GLOBAL instruments_1_supplied_name String Inverted Microscope
attribute NC_GLOBAL keywords String 95pcnt, abund, abund_lower_95pcnt_CI, abund_upper_95pcnt_CI, abundance, bco, bco-dmo, biological, biomass, cast, chemical, cruise, cruise_id, data, dataset, depth, description, dmo, erddap, latitude, location_description, longitude, lower, management, oceanography, office, preliminary, station, taxon, total, total_biomass, upper
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/4018/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/4018 (external link)
attribute NC_GLOBAL Northernmost_Northing double 33.48
attribute NC_GLOBAL param_mapping String {'4018': {'lat': 'master - latitude', 'depth': 'flag - depth', 'lon': 'master - longitude'}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/4018/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String Arizona State University
attribute NC_GLOBAL people_0_affiliation_acronym String ASU
attribute NC_GLOBAL people_0_person_name String Susanne Neuer
attribute NC_GLOBAL people_0_person_nid String 51336
attribute NC_GLOBAL people_0_role String Principal Investigator
attribute NC_GLOBAL people_0_role_type String originator
attribute NC_GLOBAL people_1_affiliation String Arizona State University
attribute NC_GLOBAL people_1_affiliation_acronym String ASU
attribute NC_GLOBAL people_1_person_name String Francesca De Martini
attribute NC_GLOBAL people_1_person_nid String 51719
attribute NC_GLOBAL people_1_role String Student
attribute NC_GLOBAL people_1_role_type String related
attribute NC_GLOBAL people_2_affiliation String Arizona State University
attribute NC_GLOBAL people_2_affiliation_acronym String ASU
attribute NC_GLOBAL people_2_person_name String Susanne Neuer
attribute NC_GLOBAL people_2_person_nid String 51336
attribute NC_GLOBAL people_2_role String Contact
attribute NC_GLOBAL people_2_role_type String related
attribute NC_GLOBAL people_3_affiliation String Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_3_affiliation_acronym String WHOI BCO-DMO
attribute NC_GLOBAL people_3_person_name String Shannon Rauch
attribute NC_GLOBAL people_3_person_nid String 51498
attribute NC_GLOBAL people_3_role String BCO-DMO Data Manager
attribute NC_GLOBAL people_3_role_type String related
attribute NC_GLOBAL project String Trophic BATS
attribute NC_GLOBAL projects_0_acronym String Trophic BATS
attribute NC_GLOBAL projects_0_description String 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.
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.
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.
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.
attribute NC_GLOBAL projects_0_end_date String 2014-09
attribute NC_GLOBAL projects_0_geolocation String Sargasso Sea, BATS site
attribute NC_GLOBAL projects_0_name String Plankton Community Composition and Trophic Interactions as Modifiers of Carbon Export in the Sargasso Sea
attribute NC_GLOBAL projects_0_project_nid String 2150
attribute NC_GLOBAL projects_0_start_date String 2010-10
attribute NC_GLOBAL publisher_name String Biological and Chemical Oceanographic Data Management Office (BCO-DMO)
attribute NC_GLOBAL publisher_type String institution
attribute NC_GLOBAL sourceUrl String (local files)
attribute NC_GLOBAL Southernmost_Northing double 30.83
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL summary String 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.
attribute NC_GLOBAL title String 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)
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL Westernmost_Easting double -64.83
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable cruise_id   String  
attribute cruise_id bcodmo_name String cruise_id
attribute cruise_id description String Official cruise identifier e.g. AE1102 = R/V Atlantic Explorer cruise number 1102.
attribute cruise_id long_name String Cruise Id
attribute cruise_id units String dimensionless
variable cast   byte  
attribute cast _FillValue byte 127
attribute cast actual_range byte 2, 38
attribute cast bcodmo_name String cast
attribute cast description String Cast number.
attribute cast long_name String Cast
attribute cast units String dimensionless
variable station   byte  
attribute station _FillValue byte 127
attribute station actual_range byte 1, 6
attribute station bcodmo_name String station
attribute station description String Station number.
attribute station long_name String Station
attribute station units String dimensionless
variable location_description   String  
attribute location_description bcodmo_name String site_descrip
attribute location_description description String Description of sampling location.
attribute location_description long_name String Location Description
attribute location_description units String dimensionless
variable latitude   double  
attribute latitude _CoordinateAxisType String Lat
attribute latitude _FillValue double NaN
attribute latitude actual_range double 30.83, 33.48
attribute latitude axis String Y
attribute latitude bcodmo_name String latitude
attribute latitude colorBarMaximum double 90.0
attribute latitude colorBarMinimum double -90.0
attribute latitude description String Latitude. Positive values = North.
attribute latitude ioos_category String Location
attribute latitude long_name String Latitude
attribute latitude nerc_identifier String https://vocab.nerc.ac.uk/collection/P09/current/LATX/ (external link)
attribute latitude standard_name String latitude
attribute latitude units String degrees_north
variable longitude   double  
attribute longitude _CoordinateAxisType String Lon
attribute longitude _FillValue double NaN
attribute longitude actual_range double -64.83, -64.17
attribute longitude axis String X
attribute longitude bcodmo_name String longitude
attribute longitude colorBarMaximum double 180.0
attribute longitude colorBarMinimum double -180.0
attribute longitude description String Longitude. Positive values = East.
attribute longitude ioos_category String Location
attribute longitude long_name String Longitude
attribute longitude nerc_identifier String https://vocab.nerc.ac.uk/collection/P09/current/LONX/ (external link)
attribute longitude standard_name String longitude
attribute longitude units String degrees_east
variable depth   double  
attribute depth _CoordinateAxisType String Height
attribute depth _CoordinateZisPositive String down
attribute depth _FillValue double NaN
attribute depth actual_range double 20.0, 100.0
attribute depth axis String Z
attribute depth bcodmo_name String depth
attribute depth colorBarMaximum double 8000.0
attribute depth colorBarMinimum double -8000.0
attribute depth colorBarPalette String TopographyDepth
attribute depth description String Sample depth.
attribute depth ioos_category String Location
attribute depth long_name String Depth
attribute depth nerc_identifier String https://vocab.nerc.ac.uk/collection/P09/current/DEPH/ (external link)
attribute depth positive String down
attribute depth standard_name String depth
attribute depth units String m
variable total_biomass   short  
attribute total_biomass _FillValue short 32767
attribute total_biomass actual_range short 0, 2957
attribute total_biomass bcodmo_name String biomass_C
attribute total_biomass description String Total biomass (ng C/L) at the particular cast and depth.
attribute total_biomass long_name String Total Biomass
attribute total_biomass units String nanograms C per Liter
variable taxon   String  
attribute taxon bcodmo_name String taxon
attribute taxon description String Name of the taxonomic group.
attribute taxon long_name String Taxon
attribute taxon units String dimensionless
variable abundance   short  
attribute abundance _FillValue short 32767
attribute abundance actual_range short 0, 3090
attribute abundance bcodmo_name String abundance
attribute abundance description String Abundance of planktonic ciliates (cells/L).
attribute abundance long_name String Abundance
attribute abundance nerc_identifier String https://vocab.nerc.ac.uk/collection/P03/current/B070/ (external link)
attribute abundance units String cells per Liter
variable abund_upper_95pcnt_CI   short  
attribute abund_upper_95pcnt_CI _FillValue short 32767
attribute abund_upper_95pcnt_CI actual_range short 5, 1414
attribute abund_upper_95pcnt_CI bcodmo_name String unknown
attribute abund_upper_95pcnt_CI description String Upper 95% confidence interval for abundance.
attribute abund_upper_95pcnt_CI long_name String Abund Upper 95pcnt CI
attribute abund_upper_95pcnt_CI units String cells per Liter
variable abund_lower_95pcnt_CI   short  
attribute abund_lower_95pcnt_CI _FillValue short 32767
attribute abund_lower_95pcnt_CI actual_range short 0, 1270
attribute abund_lower_95pcnt_CI bcodmo_name String unknown
attribute abund_lower_95pcnt_CI description String Lower 95% confidence interval for abundance.
attribute abund_lower_95pcnt_CI long_name String Abund Lower 95pcnt CI
attribute abund_lower_95pcnt_CI units String cells per Liter
variable biomass   short  
attribute biomass _FillValue short 32767
attribute biomass actual_range short 0, 1497
attribute biomass bcodmo_name String biomass_C
attribute biomass description String Biomass (ng C/L) of planktonic ciliates.
attribute biomass long_name String Biomass
attribute biomass units String nanograms C per Liter

The information in the table above is also available in other file formats (.csv, .htmlTable, .itx, .json, .jsonlCSV1, .jsonlCSV, .jsonlKVP, .mat, .nc, .nccsv, .tsv, .xhtml) via a RESTful web service.

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