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Title Sum-
Institution Dataset ID
   set  data   graph     files  public 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
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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,.odvTxt
attribute NC_GLOBAL acquisition_description String 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/\\") and

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
(.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
attribute NC_GLOBAL awards_0_award_nid String 675559
attribute NC_GLOBAL awards_0_award_number String OCE-1536776
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1536776 (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 Michael E. Sieracki
attribute NC_GLOBAL awards_0_program_manager_nid String 50446
attribute NC_GLOBAL cdm_data_type String Other
attribute NC_GLOBAL comment String Flow cytometry
PI: Douglas Bartlett (UCSD)
Version: 13 March 2017
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.
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 2017-03-14T18:19:38Z
attribute NC_GLOBAL date_modified String 2020-01-21T21:07:29Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.684323.1
attribute NC_GLOBAL Easternmost_Easting double 142.432555
attribute NC_GLOBAL geospatial_lat_max double 11.36639
attribute NC_GLOBAL geospatial_lat_min double 11.36639
attribute NC_GLOBAL geospatial_lat_units String degrees_north
attribute NC_GLOBAL geospatial_lon_max double 142.432555
attribute NC_GLOBAL geospatial_lon_min double 142.432555
attribute NC_GLOBAL geospatial_lon_units String degrees_east
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/684323 (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_nid String 684330
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 Flow Cytometer
attribute NC_GLOBAL instruments_1_dataset_instrument_nid String 684332
attribute NC_GLOBAL instruments_1_description String 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)
attribute NC_GLOBAL instruments_1_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/LAB37/ (external link)
attribute NC_GLOBAL instruments_1_instrument_name String Flow Cytometer
attribute NC_GLOBAL instruments_1_instrument_nid String 660
attribute NC_GLOBAL instruments_2_dataset_instrument_nid String 684329
attribute NC_GLOBAL instruments_2_description String 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))
attribute NC_GLOBAL instruments_2_instrument_name String Leggo Lander
attribute NC_GLOBAL instruments_2_instrument_nid String 684302
attribute NC_GLOBAL keywords String 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
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/684323/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/684323 (external link)
attribute NC_GLOBAL Northernmost_Northing double 11.36639
attribute NC_GLOBAL param_mapping String {'684323': {'lat': 'flag - latitude', 'lon': 'flag - longitude', 'ISO_DateTime_deploy': 'flag - time'}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/684323/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String University of California-San Diego
attribute NC_GLOBAL people_0_affiliation_acronym String UCSD-SIO
attribute NC_GLOBAL people_0_person_name String Douglas Bartlett
attribute NC_GLOBAL people_0_person_nid String 675562
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 Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_1_affiliation_acronym String WHOI BCO-DMO
attribute NC_GLOBAL people_1_person_name String Shannon Rauch
attribute NC_GLOBAL people_1_person_nid String 51498
attribute NC_GLOBAL people_1_role String BCO-DMO Data Manager
attribute NC_GLOBAL people_1_role_type String related
attribute NC_GLOBAL project String Mariana Perspectives
attribute NC_GLOBAL projects_0_acronym String Mariana Perspectives
attribute NC_GLOBAL projects_0_description String 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.
attribute NC_GLOBAL projects_0_end_date String 2018-08
attribute NC_GLOBAL projects_0_geolocation String Challenger Deep, Mariana Trench
attribute NC_GLOBAL projects_0_name String Patterns of Microbial Community Structure Within and Between Hadal Environments
attribute NC_GLOBAL projects_0_project_nid String 675560
attribute NC_GLOBAL projects_0_start_date String 2015-09
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 11.36639
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL subsetVariables String time,ISO_DateTime_recover,latitude,longitude
attribute NC_GLOBAL summary String Direct counts (flow cytometry) on the microbes obtained in the Leggo drop 1 Niskin bottle and the Leg drop 1 pressure-retaining sampler.
attribute NC_GLOBAL time_coverage_end String 2014-12-16T09:00:00Z
attribute NC_GLOBAL time_coverage_start String 2014-12-16T09:00:00Z
attribute NC_GLOBAL title String 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
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL Westernmost_Easting double 142.432555
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable drop_name   String  
attribute drop_name bcodmo_name String sample
attribute drop_name description String Name of the lander drop
attribute drop_name long_name String Drop Name
attribute drop_name nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute drop_name units String unitless
variable cells_per_mL   double  
attribute cells_per_mL _FillValue double NaN
attribute cells_per_mL actual_range double 14306.66667, 184064.6667
attribute cells_per_mL bcodmo_name String abundance
attribute cells_per_mL description String Number of cells per milliliter (mL)
attribute cells_per_mL long_name String Cells Per M L
attribute cells_per_mL nerc_identifier String https://vocab.nerc.ac.uk/collection/P03/current/B070/ (external link)
attribute cells_per_mL units String cells/mL
variable time   double  
attribute time _CoordinateAxisType String Time
attribute time actual_range double 1.4187204E9, 1.4187204E9
attribute time axis String T
attribute time bcodmo_name String ISO_DateTime_Local
attribute time description String Date and time (local Guam time zone) of lander deployment; formatted to ISO 8601 standard.
attribute time ioos_category String Time
attribute time long_name String ISO Date Time Deploy
attribute time source_name String ISO_DateTime_deploy
attribute time standard_name String time
attribute time time_origin String 01-JAN-1970 00:00:00
attribute time time_precision String 1970-01-01T00:00:00Z
attribute time units String seconds since 1970-01-01T00:00:00Z
variable ISO_DateTime_recover   String  
attribute ISO_DateTime_recover bcodmo_name String ISO_DateTime_Local
attribute ISO_DateTime_recover description String Date and time (local Guam time zone) of lander recovery; formatted to ISO 8601 standard.
attribute ISO_DateTime_recover long_name String ISO Date Time Recover
attribute ISO_DateTime_recover time_precision String 1970-01-01T00:00:00Z
attribute ISO_DateTime_recover units String unitless
variable latitude   double  
attribute latitude _CoordinateAxisType String Lat
attribute latitude _FillValue double NaN
attribute latitude actual_range double 11.36639, 11.36639
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 of lander deployment
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 142.432555, 142.432555
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 of lander deployment
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

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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