Accessing BCO-DMO data
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| Dataset Title: | [flow cytometry] - Direct counts (flow cytometry) on microbes obtained by Niskin bottle and pressure-retaining sampler from the Leggo Lander on R/V Falkor cruise FK141215 in the Challenger Deep, Mariana Trench in December 2014 (Patterns of Microbial Community Structure Within and Between Hadal Environments) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_684323) |
| Information: | Summary
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| FGDC
| ISO 19115
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Attributes {
s {
drop_name {
String bcodmo_name "sample";
String description "Name of the lander drop";
String long_name "Drop Name";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
String units "unitless";
}
cells_per_mL {
Float64 _FillValue NaN;
Float64 actual_range 14306.66667, 184064.6667;
String bcodmo_name "abundance";
String description "Number of cells per milliliter (mL)";
String long_name "Cells Per M L";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P03/current/B070/";
String units "cells/mL";
}
time {
String _CoordinateAxisType "Time";
Float64 actual_range 1.4187204e+9, 1.4187204e+9;
String axis "T";
String bcodmo_name "ISO_DateTime_Local";
String description "Date and time (local Guam time zone) of lander deployment; formatted to ISO 8601 standard.";
String ioos_category "Time";
String long_name "ISO Date Time Deploy";
String source_name "ISO_DateTime_deploy";
String standard_name "time";
String time_origin "01-JAN-1970 00:00:00";
String time_precision "1970-01-01T00:00:00Z";
String units "seconds since 1970-01-01T00:00:00Z";
}
ISO_DateTime_recover {
String bcodmo_name "ISO_DateTime_Local";
String description "Date and time (local Guam time zone) of lander recovery; formatted to ISO 8601 standard.";
String long_name "ISO Date Time Recover";
String time_precision "1970-01-01T00:00:00Z";
String units "unitless";
}
latitude {
String _CoordinateAxisType "Lat";
Float64 _FillValue NaN;
Float64 actual_range 11.36639, 11.36639;
String axis "Y";
String bcodmo_name "latitude";
Float64 colorBarMaximum 90.0;
Float64 colorBarMinimum -90.0;
String description "Latitude of lander deployment";
String ioos_category "Location";
String long_name "Latitude";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LATX/";
String standard_name "latitude";
String units "degrees_north";
}
longitude {
String _CoordinateAxisType "Lon";
Float64 _FillValue NaN;
Float64 actual_range 142.432555, 142.432555;
String axis "X";
String bcodmo_name "longitude";
Float64 colorBarMaximum 180.0;
Float64 colorBarMinimum -180.0;
String description "Longitude of lander deployment";
String ioos_category "Location";
String long_name "Longitude";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LONX/";
String standard_name "longitude";
String units "degrees_east";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson,.odvTxt";
String acquisition_description
"This data set is associated with PI Douglas Bartlett (NSF OCE-1536776) and
Schmidt Ocean Institute R/V Falkor cruise FK141215. The cruise occurred
December 15-21, 2014 in the Challenger Deep within the territorial waters of
the Federated States of Micronesia. During this cruise the Leggo lander was
deployed multiple times and drops 1 and 3 recovered seawater samples that were
analyzed. Additional details can be found at: [https://schmidtocean.org/cruise
/expanding-mariana-trench-perspectives/](\\\\\"https://schmidtocean.org/cruise
/expanding-mariana-trench-perspectives/\\\\\") and
[https://scripps.ucsd.edu/labs/dbartlett/contact/challenger-deep-
cruise-2014/](\\\\\"https://scripps.ucsd.edu/labs/dbartlett/contact/challenger-
deep-cruise-2014/\\\\\")
Leggo Lander Drop 1:
Time (in Guam) deployed/recovered: December 16, 9:00/19:26.
Position at deployment: 11\\u00b0 21.9836 N 142\\u00b0 25.9533 E, middle
section of the Challenger Deep.
Greatest depth of dive: approximately ~10,900 m.
In situ temperature on seafloor: 2.6\\u00b0C.
Notes: This drop recovered seawater samples from about a meter off the
seafloor.\\u00a0This included a 3 L\\u00a0Niskin bottle of seawater and ~ 150
mls of seawater collected in a pressure-retaining seawater sampler.\\u00a0The
PRS sampler held more than 81% of the in situ pressure.\\u00a0
Flow Cytometry:
Direct counts (flow cytometry) on the microbes obtained in the Leggo drop 1
Niskin bottle and the Leg drop 1 pressure-retaining sampler.\\u00a0Samples were
fixed with ~1% PFA and frozen. Later samples were removed from the -80 freezer
and thawed in the dark.
The Attune was started and a Performance Test was run with the \\\"Performance
Tracking Beads\\\"\\u00a0to check that all lasers and filters were working, and
that voltages were correct. Cleaning and decontamination was also done using
the Attune Wash solution and MilliQ water. Random samples selected from
Logan's samples were run using Instrument Settings in the Attune software.
This allows for real-time adjustments of voltages and thresholds in the
different channels to get the best resolution for that day\\u2019s run as well
as allows for quantification of instrument noise for a given day.
Once samples were thawed, 300 uL of each sample was loaded into a 96-well
U-bottom plate. 3 uL of Invitrogen Sybr-green stain (diluted to 100x in MilliQ
water) was then added to each well. The plate then incubated in the dark for
30 minutes before being run. The Sybr-green stain stains any DNA within a cell
which then fluoresces when passing the BL1 channel laser, allowing for counts
of cells.
Once instrument settings were determined for the day, the plate was loaded
into the NxT autosampler and the run was started. Samples were run at
\\\"Standard\\\" sensitivity at 100 uL/min for a total volume of 250 uL. Counts
were delayed for 15 seconds to avoid any noise or dilution that can occur when
sample starts being sipped. Once entire plate was run, I used the Attune
software to correct for noise and gate various populations within the samples.
Note: Leggo1 is the first drop of the Leggo Lander and the values reflect the
flow cytometric cell counts from its 2 liter Niskin bottle. Leggo1_PRS_day_2
is the flow cytometric cell count obtained from the pressure retaining sampler
used on the first Leggo drop, following incubation in ice water for about 36
hours after recovery.
Colony Identification:
Data from the identification of bacteria cultured from the Leggo drop 1 and
3 Niskin bottles are available as a [supplemental file](\\\\\"https://datadocs
.bco-
dmo.org/docs/bartlett/mariana_perspectives/data_docs/colony_identification.txt\\\\\")
(.txt).\\u00a0These identifications were performed using standard methods
associated with PCR amplification of the 16S rRNA gene followed by dideoxy
sequencing at Retrogen Inc.\\u00a0\\u00a0";
String awards_0_award_nid "675559";
String awards_0_award_number "OCE-1536776";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1536776";
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 "Michael E. Sieracki";
String awards_0_program_manager_nid "50446";
String cdm_data_type "Other";
String comment
"Flow cytometry
PI: Douglas Bartlett (UCSD)
Version: 13 March 2017
Notes:
Leggo1 is the first drop of the Leggo Lander and the values reflect the flow cytometric cell counts from its 2 liter Niskin bottle.
Leggo1_PRS_day_2 is the flow cytometric cell count obtained from the pressure retaining sampler used on the first Leggo drop, following incubation in ice water for about 36 hours after recovery.";
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 "2017-03-14T18:19:38Z";
String date_modified "2020-01-21T21:07:29Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.684323.1";
Float64 Easternmost_Easting 142.432555;
Float64 geospatial_lat_max 11.36639;
Float64 geospatial_lat_min 11.36639;
String geospatial_lat_units "degrees_north";
Float64 geospatial_lon_max 142.432555;
Float64 geospatial_lon_min 142.432555;
String geospatial_lon_units "degrees_east";
String history
"2024-11-21T08:37:40Z (local files)
2024-11-21T08:37:40Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_684323.html";
String infoUrl "https://www.bco-dmo.org/dataset/684323";
String institution "BCO-DMO";
String instruments_0_acronym "Niskin bottle";
String instruments_0_dataset_instrument_nid "684330";
String instruments_0_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.";
String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/";
String instruments_0_instrument_name "Niskin bottle";
String instruments_0_instrument_nid "413";
String instruments_0_supplied_name "Niskin bottle";
String instruments_1_acronym "Flow Cytometer";
String instruments_1_dataset_instrument_nid "684332";
String instruments_1_description
"Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells.
(from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm)";
String instruments_1_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB37/";
String instruments_1_instrument_name "Flow Cytometer";
String instruments_1_instrument_nid "660";
String instruments_2_dataset_instrument_nid "684329";
String instruments_2_description
"The \"Leggo Lander\" is a lander system that primarily relies on syntactic foam for buoyancy and uses iridium GPS, radio signal, strobe light and flag for surface recovery, and acoustics for underwater monitoring and instrument control. The lander has a timer with 5 control settings for various operations. It routinely measures pressure (depth) throughout its dive and temperature on the seafloor. The lander payloads include a pressure-retaining seawater sampler plus 2 liter Niskin bottle, and a camera/battery/light system that also includes a 30 liter Niskin bottle and a sea cucumber trap. With the camera payload it travels down or up the water column at about 39 meters per minute (~ 4.5 hours for a descent to the Challenger Deep at ~10,920 m).
(Description obtained from the R/V Falkor FK141215 post-cruise report (PDF))";
String instruments_2_instrument_name "Leggo Lander";
String instruments_2_instrument_nid "684302";
String keywords "bco, bco-dmo, biological, cells, cells_per_mL, chemical, data, dataset, date, deploy, dmo, drop, drop_name, erddap, iso, ISO_DateTime_recover, latitude, longitude, management, name, oceanography, office, per, preliminary, recover, time";
String license "https://www.bco-dmo.org/dataset/684323/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/684323";
Float64 Northernmost_Northing 11.36639;
String param_mapping "{'684323': {'lat': 'flag - latitude', 'lon': 'flag - longitude', 'ISO_DateTime_deploy': 'flag - time'}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/684323/parameters";
String people_0_affiliation "University of California-San Diego";
String people_0_affiliation_acronym "UCSD-SIO";
String people_0_person_name "Douglas Bartlett";
String people_0_person_nid "675562";
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 BCO-DMO";
String people_1_person_name "Shannon Rauch";
String people_1_person_nid "51498";
String people_1_role "BCO-DMO Data Manager";
String people_1_role_type "related";
String project "Mariana Perspectives";
String projects_0_acronym "Mariana Perspectives";
String projects_0_description
"Award Abstract from NSF:
The deepest portion of the ocean is present in ocean trenches, whose steep walls descend from approximately 4 miles down to depths that in some cases are close to 7 miles below the seawater surface. At these locations Earth's crust is recycled. Perhaps not surprisingly given their remoteness, deep ocean trenches are the least understood habitats in the ocean. The researchers participating in this project are working to characterize the microbes present in two of the deepest trenches present on Earth, both in the Pacific Ocean, the Kermadec Trench located north of New Zealand, and the Mariana Trench, located east and south of the island of Guam. Most of the Mariana Trench is located within the United States Mariana Trench Marine National Monument. Relatively little is known about the diversity and adaptations of the microorganisms in deep ocean trenches. An unknown fraction of the microbes present have descended from shallow waters above and are unlikely to participate in any nutrient cycles in the deep sea. Others are adapted to near freezing temperatures and up to pressures greater than 10e7 kilograms per square meter (16,000 pounds per square inch). These latter microbes perform important roles recycling organic matter. But who are they? This project is contributing to the training of diverse undergraduate and graduate students participating in research, additional undergraduate students learning about microbes inhabiting extreme environments in a web-based class, and additional graduate students and postdoctoral scientists participating in an advanced training course being offered in Antarctica.
Experiments being performed include direct counts of prokaryotes and viruses in seawater and sediments, analyses of the abundance and phylogenetic breadth of culturable heterotrophic bacteria at a range of pressures, measurements of bacterial community species diversity and richness both within and across seawater and sediment samples, as well as within and across the two trench systems, measurements of microbial activity as a function of pressure and the identification of high pressure-active cells. The data generated from these analyses are being integrated into the results of additional chemical, geological and biological measurements performed by others as a part of the National Science Foundation funded Hadal Ecosystems Studies Project. Two of the working hypotheses are that prokaryote numbers and diversity are generally positively correlated with surface productivity and proximity to the trench axis and that bacterial taxa exist which are endemic to specific trenches, present in multiple trenches and more widely distributed in deep-sea environments.";
String projects_0_end_date "2018-08";
String projects_0_geolocation "Challenger Deep, Mariana Trench";
String projects_0_name "Patterns of Microbial Community Structure Within and Between Hadal Environments";
String projects_0_project_nid "675560";
String projects_0_start_date "2015-09";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
Float64 Southernmost_Northing 11.36639;
String standard_name_vocabulary "CF Standard Name Table v55";
String subsetVariables "time,ISO_DateTime_recover,latitude,longitude";
String summary "Direct counts (flow cytometry) on the microbes obtained in the Leggo drop 1 Niskin bottle and the Leg drop 1 pressure-retaining sampler.";
String time_coverage_end "2014-12-16T09:00:00Z";
String time_coverage_start "2014-12-16T09:00:00Z";
String title "[flow cytometry] - Direct counts (flow cytometry) on microbes obtained by Niskin bottle and pressure-retaining sampler from the Leggo Lander on R/V Falkor cruise FK141215 in the Challenger Deep, Mariana Trench in December 2014 (Patterns of Microbial Community Structure Within and Between Hadal Environments)";
String version "1";
Float64 Westernmost_Easting 142.432555;
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.