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Title Sum-
Institution Dataset ID
     data        files  public 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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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
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

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.

Colony Identification:
Data from the identification of bacteria cultured from the Leggo drop 1 and
3 Niskin bottles are available as a\u00a0[supplemental
identifications were performed using standard methods associated with PCR
amplification of the 16S rRNA gene followed by dideoxy sequencing at Retrogen
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 Pressure-retained seawater (PRS) single-cell analysis
PI: Douglas Bartlett (UCSD)
Version: 13 March 2017
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.
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 dataset_current_state String Final and no updates
attribute NC_GLOBAL date_created String 2017-03-14T19:34:20Z
attribute NC_GLOBAL date_modified String 2020-01-21T21:23:26Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.684362.1
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/684362 (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 684369
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_description String Cells were sorted using a flow cytometer
attribute NC_GLOBAL instruments_1_dataset_instrument_nid String 684372
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_acronym String Thermal Cycler
attribute NC_GLOBAL instruments_2_dataset_instrument_description String Multiple displacement amplification and 16S rRNA gene PCR and sequencing were performed
attribute NC_GLOBAL instruments_2_dataset_instrument_nid String 684373
attribute NC_GLOBAL instruments_2_description String 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)
attribute NC_GLOBAL instruments_2_instrument_name String PCR Thermal Cycler
attribute NC_GLOBAL instruments_2_instrument_nid String 471582
attribute NC_GLOBAL instruments_3_dataset_instrument_nid String 684368
attribute NC_GLOBAL instruments_3_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_3_instrument_name String Leggo Lander
attribute NC_GLOBAL instruments_3_instrument_nid String 684302
attribute NC_GLOBAL keywords String bco, bco-dmo, biological, chemical, classification, data, dataset, dmo, erddap, management, oceanography, office, partial, partial_16S_seq, preliminary, seq, silva, SILVA_classification
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/684362/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/684362 (external link)
attribute NC_GLOBAL param_mapping String {'684362': {}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/684362/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 standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL summary String Culture-independent identification of bacteria present in the pressure-retaining seawater (PRS) sampler deployed during Leggo drop 1.
attribute NC_GLOBAL title String 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
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.5
variable SILVA_classification   String  
attribute SILVA_classification bcodmo_name String taxon
attribute SILVA_classification description String SILVA classification
attribute SILVA_classification long_name String SILVA Classification
attribute SILVA_classification units String unitless
variable partial_16S_seq   String  
attribute partial_16S_seq bcodmo_name String sequence
attribute partial_16S_seq description String Partial 16S rRNA gene sequence
attribute partial_16S_seq long_name String Partial 16 S Seq
attribute partial_16S_seq units String unitless

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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