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|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
|Row Type||Variable Name||Attribute Name||Data Type||Value|
|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
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
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.
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_funder_name||String||NSF Division of Ocean Sciences|
|attribute||NC_GLOBAL||awards_0_program_manager||String||Michael E. Sieracki|
|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||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||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_1_dataset_instrument_description||String||Cells were sorted using a flow cytometer|
|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.
|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_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_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||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||people_0_affiliation||String||University of California-San Diego|
|attribute||NC_GLOBAL||people_1_affiliation||String||Woods Hole Oceanographic Institution|
|attribute||NC_GLOBAL||people_1_role||String||BCO-DMO Data Manager|
|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_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||publisher_name||String||Biological and Chemical Oceanographic Data Management Office (BCO-DMO)|
|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||partial_16S_seq||description||String||Partial 16S rRNA gene sequence|
|attribute||partial_16S_seq||long_name||String||Partial 16 S Seq|
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.