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Dataset Title:  Culture-independent identification of bacteria present in the pressure-
retaining seawater (PRS) sampler deployed during Leggo drop 1 from R/V Falkor
cruise FK141215 in the Challenger Deep, Mariana Trench in December 2014
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Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_684362)
Information:  Summary ? | License ? | ISO 19115 | Metadata | Background (external link) | Files
 
Variable ?   Optional
Constraint #1 ?
Optional
Constraint #2 ?
   Minimum ?
 
   Maximum ?
 
 SILVA_classification (unitless) ?          "Bacteria;Bacteroid..."    "Bacteria;Proteobac..."
 partial_16S_seq (unitless) ?          "AAAGAGTTCGTAGGCTGN..."    "TTGGGTTTAAAGGGTCCG..."
 
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The Dataset Attribute Structure (.das) for this Dataset

Attributes {
 s {
  SILVA_classification {
    String bcodmo_name "taxon";
    String description "SILVA classification";
    String long_name "SILVA Classification";
    String units "unitless";
  }
  partial_16S_seq {
    String bcodmo_name "sequence";
    String description "Partial 16S rRNA gene sequence";
    String long_name "Partial 16 S Seq";
    String units "unitless";
  }
 }
  NC_GLOBAL {
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
    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
 
PRS data:  
 The culture independent identification of the bacteria present in the
pressure-retaining seawater (PRS) sampler deployed during Leggo drop 1. This
involved cell sorting, multiple displacement amplification, and 16S rRNA gene
PCR and sequencing. More complete details are described in:
 
Leon-Zayas, R., Novotny, M., Podell, S., Shepard, C. M., Berkenpas, E.,
Nikolenko, S., Pevzner, P., Lasken, R. S. and Bartlett, D. H. 2015. Single
cells within the Puerto Rico Trench suggest hadal adaptation of microbial
lineages. Appl. Environ. Microbiol. 81: 8265-8276.
doi:[10.1128/AEM.01659-15](\\\\\"https://dx.doi.org/10.1128/AEM.01659-15\\\\\")
 
Colony Identification:  
 Data from the identification of bacteria cultured from the Leggo drop 1 and
3 Niskin bottles are available as a\\u00a0[supplemental
file](\\\\\"https://datadocs.bco-
dmo.org/docs/bartlett/mariana_perspectives/data_docs/colony_identification.txt\\\\\")\\u00a0(.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 
"Pressure-retained seawater (PRS) single-cell analysis 
 PI: Douglas Bartlett (UCSD) 
 Version: 13 March 2017 
 Note: 
  These are the four types of deep-sea microbes identified in the pressure-retained seawater sample obtained during the first drop of the Leggo lander.  
  The cells were identified following cell sorting, MDA amplification, and 16S rRNA gene screening.";
    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 dataset_current_state "Final and no updates";
    String date_created "2017-03-14T19:34:20Z";
    String date_modified "2020-01-21T21:23:26Z";
    String defaultDataQuery "&time<now";
    String doi "10.1575/1912/bco-dmo.684362.1";
    String history 
"2021-10-24T12:48:27Z (local files)
2021-10-24T12:48:27Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_684362.html";
    String infoUrl "https://www.bco-dmo.org/dataset/684362";
    String institution "BCO-DMO";
    String instruments_0_acronym "Niskin bottle";
    String instruments_0_dataset_instrument_nid "684369";
    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_description "Cells were sorted using a flow cytometer";
    String instruments_1_dataset_instrument_nid "684372";
    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_acronym "Thermal Cycler";
    String instruments_2_dataset_instrument_description "Multiple displacement amplification and 16S rRNA gene PCR and sequencing were performed";
    String instruments_2_dataset_instrument_nid "684373";
    String instruments_2_description 
"General term for a laboratory apparatus commonly used for performing polymerase chain reaction (PCR). The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps.

(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)";
    String instruments_2_instrument_name "PCR Thermal Cycler";
    String instruments_2_instrument_nid "471582";
    String instruments_3_dataset_instrument_nid "684368";
    String instruments_3_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_3_instrument_name "Leggo Lander";
    String instruments_3_instrument_nid "684302";
    String keywords "bco, bco-dmo, biological, chemical, classification, data, dataset, dmo, erddap, management, oceanography, office, partial, partial_16S_seq, preliminary, seq, silva, SILVA_classification";
    String license "https://www.bco-dmo.org/dataset/684362/license";
    String metadata_source "https://www.bco-dmo.org/api/dataset/684362";
    String param_mapping "{'684362': {}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/684362/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)";
    String standard_name_vocabulary "CF Standard Name Table v55";
    String summary "Culture-independent identification of bacteria present in the pressure-retaining seawater (PRS) sampler deployed during Leggo drop 1.";
    String title "Culture-independent identification of bacteria present in the pressure-retaining seawater (PRS) sampler deployed during Leggo drop 1 from R/V Falkor cruise FK141215 in the Challenger Deep, Mariana Trench in December 2014";
    String version "1";
    String xml_source "osprey2erddap.update_xml() v1.5";
  }
}

 

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tabledap lets you request a data subset, a graph, or a map from a tabular dataset (for example, buoy data), via a specially formed URL. tabledap uses the OPeNDAP (external link) Data Access Protocol (DAP) (external link) and its selection constraints (external link).

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.


 
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