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| Dataset Title: | [Sediment trap gel images] - Sediment trap gel images of settled particles that were collected from the Sargasso Sea between 2013 and 2014. (Rapid, Autonomous Particle Flux Observations in the Oligotrophic Ocean) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_728395) |
| Information: | Summary
| License
| ISO 19115
| Metadata
| Background
| Files
|
Attributes {
s {
Year {
Int16 _FillValue 32767;
Int16 actual_range 2013, 2014;
String bcodmo_name "year";
String description "Year images were collected; yyyy";
String long_name "Year";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/YEARXXXX/";
String units "unitless";
}
Month {
String bcodmo_name "month";
String description "Month images were collected";
String long_name "Month";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/MNTHXXXX/";
String units "unitless";
}
Image_zip_download_link {
String bcodmo_name "file_link";
String description "Download link to the zip file of images from the respective year and month";
String long_name "Image Zip Download Link";
String units "unitless";
}
Zip_size {
String bcodmo_name "file_size";
String description "Zip file size";
String long_name "Zip Size";
String units "unitless";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
String acquisition_description
"Particle flux measurements and images of settled particles were obtained from
neutrally-buoyant sediment trap (NBST) deployments during a series of five
short cruises in conjunction with the Bermuda Atlantic Time-series Study
(BATS) in the Sargasso Sea from July 2013 to March 2014. The NBST platforms
were constructed around Sounding Oceanographic Lagrangian Observer (SOLO)
profiling floats and carried four sediment trap tubes with areas of 0.0113 m2
(see\\u00a0[https://www.bco-dmo.org/instrument/632](\\\\\"http://www.bco-
dmo.org/instrument/632\\\\\")). NBSTs were programmed to descend to a single
measurement depth (150, 200, 300 or 500 m),\\u00a0sample\\u00a0for a 2\\u20133 d
period, and then ascend to the surface for recovery. Details are described
fully in Durkin et al. (2015) and Estapa et al. (2017).
One tube on each NBST was loaded with a polyacrylamide gel insert to preserve
sizes and shapes of settling particles for imaging. Polyacrylamide gel layers
were prepared in 11-cm diameter polycarbonate jars using methods described in
previous studies (Ebersbach and Trull, 2008; Lundsgaard, 1995; McDonnell and
Buesseler, 2010) with slight modifications. To prepare 12% polyacrylamide gel,
7.5 g of sea salts was dissolved\\u00a0into\\u00a0400 mL of surface seawater
from Vineyard Sound, MA, USA and filtered through a 0.2-\\u03bcm polycarbonate
filter. The filtered brine was boiled for 15 min to reduce the oxygen content
and reduce the brine volume to 350 mL. The solution was bubbled with nitrogen
gas through glass pipet tips attached to a pressurized tank while the solution
cooled to room temperature. The container of brine was then placed in an ice
bath on a stir plate and 150 mL of 40% acrylamide solution and 1 g of ammonium
persulfate was added to the solution while stirring. After the ammonium
persulfate dissolved, 1 mL of tetramethylethylenediamine was added to catalyze
polymerization. Gels were stored at 4\\u00b0C until use. Prior to deployment, a
jar containing a layer of polyacrylamide gel was fitted to the bottom of the
trap tube and the tube was filled with filtered seawater. Upon recovery and a
settling period of >1 h, the overlying seawater was pumped down to the top of
the gel jar and the gel insert was removed and stored at 4\\u00b0C until
analysis. One additional gel trap tube was identically prepared
and\\u00a0processed,\\u00a0but was kept covered in the ship's lab during the
deployment period to serve as a process blank.
A series of photomicrographs\\u00a0was\\u00a0taken of each gel trap at 7\\u00d7,
16\\u00d7, and 63\\u00d7 magnifications using an Olympus SZX12 stereomicroscope
with an Olympus Qcolor 5 camera attachment and QCapture imaging software. At a
magnification of 7\\u00d7, 49\\u201367% of the gel surface area was imaged in
16\\u201322 fields of view (0.1 pixels per \\u03bcm) in a single focal plane. At
16\\u00d7, 17\\u201338% of the gel surface area was imaged in randomly
distributed fields of view (0.236 pixels per \\u03bcm) across the entire gel
surface. At this magnification, a single focal plane could not capture every
particle within one field of view; large particles typically accumulated
toward the bottom of the gel layer and relatively small particles were
distributed in more focal planes throughout the gel layer. To reduce the
underestimation of small particle abundance, two images were taken from
different focal planes in each field of view (27\\u201360 fields, 54\\u2013120
images). At 63\\u00d7, 0.5\\u20130.8% of the total gel surface area was imaged
(12\\u201320 fields of view). Images were taken in cross-sections spanning the
diameter of the gel. The purpose of imaging a small percentage of the gel at
high magnification was to accurately quantify the abundance of small
particles. Between 11 and 15 focal planes were imaged in each field of view
(0.746 pixels per \\u03bcm), depending on the depth of the gel and how many
distinct focal planes contained particles. Imaging the same particle twice
within one field of view was avoided by ensuring that focal planes did not
include overlapping particles. Between 132 and 220 images were captured of
each gel at 63\\u00d7 magnification. By imaging at three magnifications,
between 240 and 360 images were captured of each gel. Image files are named as
\\u2018month_trapdepth_magnification_fieldofview_focalplane.tiff\\u2019,
with\\u00a0field\\u00a0of view represented as sequential integers and focal
plane represented as sequential letters. Recognizable zooplankton, presumed to
have actively entered the gel traps, were also counted manually in 40 fields
of view per gel at 32\\u00d7 magnification.
Flux measurements and images are not available at 200 m for the July 5, 2013
deployment due to failure of the lid closure mechanisms on all tubes.";
String awards_0_award_nid "644826";
String awards_0_award_number "OCE-1406552";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1406552";
String awards_0_funder_name "NSF Division of Ocean Sciences";
String awards_0_funding_acronym "NSF OCE";
String awards_0_funding_source_nid "355";
String awards_0_program_manager "Henrietta N Edmonds";
String awards_0_program_manager_nid "51517";
String cdm_data_type "Other";
String comment
"Sediment Trap - Gel Images
M. Estapa and K. Buesseler, PIs
Version 26 February 2018";
String Conventions "COARDS, CF-1.6, ACDD-1.3";
String creator_email "info@bco-dmo.org";
String creator_name "BCO-DMO";
String creator_type "institution";
String creator_url "https://www.bco-dmo.org/";
String data_source "extract_data_as_tsv version 2.3 19 Dec 2019";
String date_created "2018-02-26T20:25:17Z";
String date_modified "2018-11-15T18:51:47Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.734359";
String history
"2024-11-23T17:22:07Z (local files)
2024-11-23T17:22:07Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_728395.html";
String infoUrl "https://www.bco-dmo.org/dataset/728395";
String institution "BCO-DMO";
String instruments_0_acronym "NBST";
String instruments_0_dataset_instrument_description "Used to measure particles";
String instruments_0_dataset_instrument_nid "733293";
String instruments_0_description "In general, sediment traps are specially designed containers deployed in the water column for periods of time to collect particles from the water column falling toward the sea floor. The Neutrally Buoyant Sediment Trap (NBST) was designed by researchers at Woods Hole Oceanographic Institution. The central cylinder of the NBST controls buoyancy and houses a satellite transmitter. The other tubes collect sediment as the trap drifts in currents at a predetermined depth. The samples are collected when the tubes snap shut before the trap returns to the surface. (more: https://www.whoi.edu/instruments/viewInstrument.do?id=10286)";
String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/33/";
String instruments_0_instrument_name "Neutrally Buoyant Sediment Trap";
String instruments_0_instrument_nid "632";
String instruments_0_supplied_name "NBST";
String instruments_1_dataset_instrument_description "Used to take photomicrographs";
String instruments_1_dataset_instrument_nid "729425";
String instruments_1_description "Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of visible light. Includes conventional and inverted instruments. Also called a \"light microscope\".";
String instruments_1_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB05/";
String instruments_1_instrument_name "Microscope-Optical";
String instruments_1_instrument_nid "708";
String instruments_1_supplied_name "Olympus SZX12 stereomicroscope with an Olympus Qcolor 5 camera attachment";
String keywords "bco, bco-dmo, biological, chemical, data, dataset, dmo, download, erddap, image, Image_zip_download_link, link, management, month, oceanography, office, preliminary, size, year, zip, Zip_size";
String license "https://www.bco-dmo.org/dataset/728395/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/728395";
String param_mapping "{'728395': {}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/728395/parameters";
String people_0_affiliation "Skidmore College";
String people_0_person_name "Margaret L. Estapa";
String people_0_person_nid "644830";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "Woods Hole Oceanographic Institution";
String people_1_affiliation_acronym "WHOI";
String people_1_person_name "Kenneth O. Buesseler";
String people_1_person_nid "50522";
String people_1_role "Co-Principal Investigator";
String people_1_role_type "originator";
String people_2_affiliation "Skidmore College";
String people_2_person_name "Margaret L. Estapa";
String people_2_person_nid "644830";
String people_2_role "Contact";
String people_2_role_type "related";
String people_3_affiliation "Woods Hole Oceanographic Institution";
String people_3_affiliation_acronym "WHOI BCO-DMO";
String people_3_person_name "Hannah Ake";
String people_3_person_nid "650173";
String people_3_role "BCO-DMO Data Manager";
String people_3_role_type "related";
String project "RapAutParticleFlux";
String projects_0_acronym "RapAutParticleFlux";
String projects_0_description
"Particles settling into the deep ocean remove carbon and biologically-important trace elements from sunlit, productive surface waters and from contact with the atmosphere over short timescales. A shifting balance among physical, chemical, and biological processes determines the ultimate fate of most particles at depths between 100 and 1,000 m, where fluxes are hardest to measure. Our challenge is to expand the number of particle flux observations in the critical \"twilight zone\", something that has proven elusive with ship-based “snapshots” that have lengths of, at most, a few weeks. Here, we propose an optical, transmissometer-based method to make particle flux observations from autonomous, biogeochemical profiling floats. Novel developments in data interpretation, sensor operation, and platform control now allow flux measurements at hourly resolution and give us observational access to the water-column processes driving particle flux over short timescales. The sensors and float platforms that we propose to use are simple, robust, and commercially-available, making them immediately compatible with community-scale efforts to implement other float-based biogeochemical measurements.
We have two main goals: First, we will quantify particulate organic carbon (POC) flux using float-based optical measurements by validating our observations against fluxes measured directly with neutrally-buoyant, drifting sediment traps. Second, we will evaluate the contribution of rapid export events to total POC fluxes in the oligotrophic ocean by using a biogeochemical profiling float to collect nearly-continuous, depth-resolved flux measurements and coupled, water-column bio-optical profiles.
To achieve these goals, we will implement a work plan consisting of 1) a set of laboratory-based sensor calibration experiments to determine detection limits and evaluate sensitivity to particle size; 2) a series of four sediment trap and biogeochemical float co-deployments during which we will collect POC flux and field calibration data; and 3) a long-term sampling and analysis period (approximately 1 year) during which data will be returned by satellite from the biogeochemical float. We will conduct calibration fieldwork in conjunction with monthly Bermuda Atlantic Time-series Study (BATS) cruises, taking advantage of the timeseries measurements and the context provided by the 25-year record of POC flux at that site. The data returned by the float will comprise the first quantitative particle flux observations made at high-enough temporal resolution to interpret in the context of short-term, upper-ocean production events.";
String projects_0_end_date "2014-11";
String projects_0_geolocation "Sargasso Sea";
String projects_0_name "Rapid, Autonomous Particle Flux Observations in the Oligotrophic Ocean";
String projects_0_project_nid "644827";
String projects_0_start_date "2013-07";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
String standard_name_vocabulary "CF Standard Name Table v55";
String summary "Sinking particle sizes span many orders of magnitude and the relative influence of small particles on carbon export compared to large particles has not been resolved. To determine the influence of particle size on carbon export, the flux of both small (11\\u201364 \\u03bcm) and large (>64 \\u03bcm) particles in the upper mesopelagic was examined during five cruises of the Bermuda Atlantic Time Series (BATS) in the Sargasso Sea using neutrally buoyant sediment traps mounted with tubes containing polyacrylamide gel layers to preserve sizes and shapes of sinking particles. Microphotographic images of gels were collected and used to determine particle size distributions.";
String title "[Sediment trap gel images] - Sediment trap gel images of settled particles that were collected from the Sargasso Sea between 2013 and 2014. (Rapid, Autonomous Particle Flux Observations in the Oligotrophic Ocean)";
String version "1";
String xml_source "osprey2erddap.update_xml() v1.3";
}
}
Data Access Protocol (DAP) and its
selection constraints.
The URL specifies what you want: the dataset, a description of the graph or the subset of the data, and the file type for the response.
Tabledap request URLs must be in the form
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/datasetID.fileType{?query}
For example,
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/pmelTaoDySst.htmlTable?longitude,latitude,time,station,wmo_platform_code,T_25&time>=2015-05-23T12:00:00Z&time<=2015-05-31T12:00:00Z
Thus, the query is often a comma-separated list of desired variable names,
followed by a collection of
constraints (e.g., variable<value),
each preceded by '&' (which is interpreted as "AND").
For details, see the tabledap Documentation.