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Title Sum-
Institution Dataset ID
     data   graph     files  public Microbial cell abundance,carbon fixation rates, and nitrate concentrations during shipboard
incubations of vent fluids at the diffuse-flow vent Crab Spa, East Pacific Rise on RV/Atlantis
cruise AT37-12, May 2017
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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 During Alvin Dive 4905, May 8, 2017, 5 major samples were collected at the
diffuse-flow vent Crab Spa. The fluid from these samplers was used in an on-
deck Vent-SID incubation. The purpose of the incubation was to simulate a sea-
floor incubation of the Vent-SID. Upon arrival of majors on the ship, we
transferred fluid from the majors into N2 flushed 1L Restek bags. The bags
were stored at 4\u02daC and taken out as needed for setting up a new Vent-SID
incubation. In total,\u00a0six incubations were conducted, all at

Microbial cell counts: Samples for cell numbers were fixed with formaldehyde
(1% final concentration) and then counted on the board the ship after staining
with acridine orange by fluorescence microscopy as described in McNichol et
al. (2016).

Carbon fixation rates: 13C-labeled bicarbonate was added to the incubation
chambers to assess chemoautotrophic production.\u00a0At the beginning and the
end of the incubation, fluids were filtered onto pre combusted GFF filters,
which were frozen until analysis back in the shore lab. Gas chromatography
combustion (Fisons 1108 Elemental Analyzer equipped with a Costech \"Zero
Blank\" sample carousel) coupled to an isotope ratio mass spectrometer (GC-
IRMS) (Finnigan-MAT Conflo-II interface attached to a DeltaPlus Isotope Ratio
Mass Spectrometer) was used to measure the incorporation of 13C-labelled
bicarbonate into biomass during the incubations to determine chemoautotrophic

Nitrate concentrations:\u00a0\u00a0Vent fluid from the Crab Spa site was
incubated on the deck of the ship in the Vent-SID reaction chamber, in the
dark at a temperature of 25(+/- 2)\u00b0C. Incubations consisted of a vent
fluid with added NO3- (10 \u00b5mol/L), NO2- (1 \u00b5mol/L) and H13CO3- (0.7
mmol/L) and time-point samples were taken for nitrate+nitrite measurements at
0, 3, and 6 hours. Six incubations were conducted that varied in combinations
of 15NO3-/14NO3 or 15NO2-/14NO2-, keeping the total concentration of added
NO3- and NO2- constant across incubations.\u00a0

Nitrate concentrations were measured in time-point samples utilizing the
vanadium(III) reduction of nitrate and nitrite method described by Braman and
Hendrix, 1989. Samples were injected into a heated Vanadium acid solution
whereby NO3- and NO2- were reduced to NOx gases. The NOx then passed into a
Teledyne T200 NOx analyzer where a photodetector measured the light produced
from the chemiluminescent reaction of NOx and instrument generated ozone.

After initial collection, vent fluid samples were stored in 15 mL conical
tubes at -20C until analyzed on the Teledyne NOx analyzer. Once thawed,
samples were injected using Hamilton 1700 series gastight syringes and Nitrate
concentrations were calculated alongside standards generated from a Ricca
Nitrate Nitrogen Standard (CAT#5459-16, 1000 ppm N, 4427 ppm NO3). The series
of standards ranged from 1 uM to 50 uM and were made up by diluting the Ricca
standard in Milli-Q water.

Peak Simple Version 4.49 was used to generate chromatographs from the
photodetector and raw data was further processed in Microsoft Excel.
attribute NC_GLOBAL awards_0_award_nid String 685772
attribute NC_GLOBAL awards_0_award_number String OCE-1559198
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1559198 (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 awards_1_award_nid String 685780
attribute NC_GLOBAL awards_1_award_number String OCE-1559042
attribute NC_GLOBAL awards_1_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1559042 (external link)
attribute NC_GLOBAL awards_1_funder_name String NSF Division of Ocean Sciences
attribute NC_GLOBAL awards_1_funding_acronym String NSF OCE
attribute NC_GLOBAL awards_1_funding_source_nid String 355
attribute NC_GLOBAL awards_1_program_manager String Michael E. Sieracki
attribute NC_GLOBAL awards_1_program_manager_nid String 50446
attribute NC_GLOBAL cdm_data_type String Other
attribute NC_GLOBAL comment String Incubations: cell counts, carbon fixation rates, nitrates
R/V Atlantis, AT37-12 shipboard incubations of vent fluids from Crab Spa site, East Pacific Rise, May 2017
PI: S. Sievert (WHOI)
version date: 2020-1-30
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 2020-01-30T14:33:34Z
attribute NC_GLOBAL date_modified String 2020-07-02T19:28:18Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.26008/1912/bco-dmo.788911.1
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/788911 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_acronym String IR Mass Spec
attribute NC_GLOBAL instruments_0_dataset_instrument_description String Used for carbon fixation measurements.
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 788944
attribute NC_GLOBAL instruments_0_description String The Isotope-ratio Mass Spectrometer is a particular type of mass spectrometer used to measure the relative abundance of isotopes in a given sample (e.g. VG Prism II Isotope Ratio Mass-Spectrometer).
attribute NC_GLOBAL instruments_0_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/LAB16/ (external link)
attribute NC_GLOBAL instruments_0_instrument_name String Isotope-ratio Mass Spectrometer
attribute NC_GLOBAL instruments_0_instrument_nid String 469
attribute NC_GLOBAL instruments_0_supplied_name String DeltaPlus Isotope Ratio Mass Spectrometer with attached Finnigan-MAT Conflo-II interface
attribute NC_GLOBAL instruments_1_dataset_instrument_description String Used for microbial cell counts.
attribute NC_GLOBAL instruments_1_dataset_instrument_nid String 788945
attribute NC_GLOBAL instruments_1_description String Instruments that generate enlarged images of samples using the phenomena of fluorescence and phosphorescence instead of, or in addition to, reflection and absorption of visible light. Includes conventional and inverted instruments.
attribute NC_GLOBAL instruments_1_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/LAB06/ (external link)
attribute NC_GLOBAL instruments_1_instrument_name String Microscope-Fluorescence
attribute NC_GLOBAL instruments_1_instrument_nid String 695
attribute NC_GLOBAL instruments_2_dataset_instrument_description String Used for carbon fixation measurements
attribute NC_GLOBAL instruments_2_dataset_instrument_nid String 788943
attribute NC_GLOBAL instruments_2_description String Instruments that quantify carbon, nitrogen and sometimes other elements by combusting the sample at very high temperature and assaying the resulting gaseous oxides. Usually used for samples including organic material.
attribute NC_GLOBAL instruments_2_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/LAB01/ (external link)
attribute NC_GLOBAL instruments_2_instrument_name String Elemental Analyzer
attribute NC_GLOBAL instruments_2_instrument_nid String 546339
attribute NC_GLOBAL instruments_2_supplied_name String • Fisons 1108 Elemental Analyzer equipped with a Costech "Zero Blank" sample carousel
attribute NC_GLOBAL instruments_3_dataset_instrument_description String Used to generate chromatographs from the photodetector and thus measure nitrate concentrations.
attribute NC_GLOBAL instruments_3_dataset_instrument_nid String 806816
attribute NC_GLOBAL instruments_3_description String Instruments that quantify carbon, nitrogen and sometimes other elements by combusting the sample at very high temperature and assaying the resulting gaseous oxides. Usually used for samples including organic material.
attribute NC_GLOBAL instruments_3_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/LAB01/ (external link)
attribute NC_GLOBAL instruments_3_instrument_name String Elemental Analyzer
attribute NC_GLOBAL instruments_3_instrument_nid String 546339
attribute NC_GLOBAL instruments_3_supplied_name String Teledyne T200 NOx analyzer with a SRI Model 333 Peak Simple Chromatography Data System
attribute NC_GLOBAL instruments_4_dataset_instrument_description String A Vent-SID, Vent-Submersible Incubation Device, was used for on-deck incubations. It draws seawater and microbes into incubation chambers and measures the biochemical business going on under natural conditions. For further description of this device, see https://www.whoi.edu/oceanus/feature/bringing-a-lab-to-the-seafloor/.
attribute NC_GLOBAL instruments_4_dataset_instrument_nid String 788942
attribute NC_GLOBAL instruments_4_description String A device mounted on a ship that holds water samples under conditions of controlled temperature or controlled temperature and illumination.
attribute NC_GLOBAL instruments_4_instrument_name String Shipboard Incubator
attribute NC_GLOBAL instruments_4_instrument_nid String 629001
attribute NC_GLOBAL instruments_4_supplied_name String Vent-SID
attribute NC_GLOBAL keywords String abund, bco, bco-dmo, biological, carbon, carbon_fix, cell, cell_abund, chemical, data, dataset, dmo, elapsed, erddap, fix, incubation, management, nox, oceanography, office, preliminary, time, time_elapsed
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/788911/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/788911 (external link)
attribute NC_GLOBAL param_mapping String {'788911': {}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/788911/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_0_affiliation_acronym String WHOI
attribute NC_GLOBAL people_0_person_name String Stefan M Sievert
attribute NC_GLOBAL people_0_person_nid String 51416
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 University of Maine
attribute NC_GLOBAL people_1_person_name String Dr Jeremy Rich
attribute NC_GLOBAL people_1_person_nid String 685778
attribute NC_GLOBAL people_1_role String Co-Principal Investigator
attribute NC_GLOBAL people_1_role_type String originator
attribute NC_GLOBAL people_2_affiliation String Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_2_affiliation_acronym String WHOI BCO-DMO
attribute NC_GLOBAL people_2_person_name String Nancy Copley
attribute NC_GLOBAL people_2_person_nid String 50396
attribute NC_GLOBAL people_2_role String BCO-DMO Data Manager
attribute NC_GLOBAL people_2_role_type String related
attribute NC_GLOBAL project String vent O2 NO3 roles
attribute NC_GLOBAL projects_0_acronym String vent O2 NO3 roles
attribute NC_GLOBAL projects_0_description String NSF award abstract:
Deep-sea hydrothermal vents, first discovered in 1977, are exemplary ecosystems where microbial chemosynthesis rather than photosynthesis is the primary source of organic carbon. Chemosynthetic microorganisms use the energy generated by oxidizing reduced inorganic chemicals contained in the vent fluids, like hydrogen sulfide or hydrogen gas, to convert carbon dioxide (CO2) into cell material. By doing so, they effectively transfer the energy from a geothermal source to higher trophic levels, in the process supporting the unique and fascinating ecosystems that are characterized by high productivity - oases in the otherwise barren deep ocean landscape. While the general view of the functioning of these ecosystems is established, there are still major gaps in our understanding of the microbiology and biogeochemistry of these systems. Particularly lacking are studies measuring rates of microbial activity in situ, which is ultimately needed to understand production of these ecosystems and to assess their impact on global biogeochemical cycles. This project makes use of the Vent-Submersible Incubation Device (Vent-SID), a robotic micro-laboratory that was recently developed and tested in the field. This instrument makes it possible for the first time to determine rates of carbon fixation at both in situ pressures and temperatures, revolutionizing the way we conduct microbial biogeochemical investigations at deep-sea hydrothermal vents. This is an interdisciplinary and collaborative effort between two US and foreign institutions, creating unique opportunities for networking and to foster international collaborations. This will also benefit two graduate students working in the project, who will get exposed to a wide range of instrumentation and scientific fields, facilitating their interdisciplinary education. In collaboration with Dr. Nitzan Resnick, academic dean of The Sage School, an elementary school outreach program will be developed and a long-term partnership with the school established. Further, a cruise blog site to disseminate the research to schools and the broader public will be set up. The results will be the topic of media coverage as well as be integrated into coursework and webpages existing either in the PI's labs or at the institution.
This project is using a recently developed robotic micro-laboratory, the Vent-SID, to measure rates of chemoautotrophic production and to determine the relative importance of oxygen and nitrate in driving chemosynthesis at deep-sea hydrothermal vents at in situ pressures and temperatures and to tackle the following currently unresolved science objectives: 1) obtain in situ rates of chemoautotrophic carbon fixation, 2) obtain in situ nitrate reduction rate measurements, and 3) directly correlate the measurement of these processes with the expression of key genes involved in carbon and energy metabolism. Although recent data suggests that nitrate reduction either to N2 (denitrification) or to NH4+ (dissimilatory reduction of nitrate to ammonium) might be responsible for a significant fraction of chemoautotrophic production, NO3-reduction rates have never been measured in situ at hydrothermal vents. The researchers hypothesize that chemoautrophic growth is strongly coupled to nitrate respiration in vent microbial communities. During a cruise that will take place approximately 12 months into the project (~Feb 2017), the researchers will carry out a total of 4 deployments of the Vent-SID as well as ancillary sampling collection at the 9°46N to 9°53N segment of the East Pacific Rise. They will focus efforts on two diffuse-flow vent sites, "Crab Spa" and "Teddy Bear". "Crab Spa" is a diffuse flow vent site (T: 25°C) that has been used as a model system to gain insights into chemoautotrophic processes and has been frequently sampled over the last several years. This vent site has been very well characterized, both geochemically and microbiologically, providing excellent background data for the proposed process oriented studies. "Teddy Bear" is a diffuse-flow site that was discovered in Jan 2014, and it has a lower temperature (T: 12°C), making it a good comparative site. The researchers will perform a number of short duration time-course incubations to assess the role of different environmental parameters that have been identified as likely key variables (e.g., O2, temperature, NO3-), and to link these process rate measurements to the expression of functional genes using metatranscriptomic analyses. This study will be the first attempt to measure critical metabolic processes of hydrothermal vent microbial assemblages under critical in situ conditions and to assess the quantitative importance of electron donor and acceptor pathways in situ. In the future, it is envisioned that the Vent-SID will become a routine application by the oceanographic community for measuring time series rates of relevant metabolic processes at hydrothermal vents under in situ pressures and vent fluid temperatures.
attribute NC_GLOBAL projects_0_end_date String 2019-04
attribute NC_GLOBAL projects_0_geolocation String Deep-Sea hydrothermal vent field at 9 deg N on the East Pacific Rise
attribute NC_GLOBAL projects_0_name String Collaborative Research: Environmental Drivers of Chemoautotrophic Carbon Production at Deep-Sea Hydrothermal Vents - Comparative Roles of Oxygen and Nitrate
attribute NC_GLOBAL projects_0_project_nid String 685773
attribute NC_GLOBAL projects_0_start_date String 2016-05
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 Microbial cell abundance, carbon fixation rates, and nitrate concentrations during shipboard incubations of vent fluids at the diffuse-flow vent Crab Spa, East Pacific Rise in the Eastern Tropical North Pacific (ETNP) on RV/Atlantis cruise AT37-12, May 2017.
attribute NC_GLOBAL title String Microbial cell abundance,carbon fixation rates, and nitrate concentrations during shipboard incubations of vent fluids at the diffuse-flow vent Crab Spa, East Pacific Rise on RV/Atlantis cruise AT37-12, May 2017
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.5
variable incubation   byte  
attribute incubation _FillValue byte 127
attribute incubation actual_range byte 1, 6
attribute incubation bcodmo_name String sample
attribute incubation description String incubation run identifier
attribute incubation long_name String Incubation
attribute incubation nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute incubation units String unitless
variable time_elapsed   byte  
attribute time_elapsed _FillValue byte 127
attribute time_elapsed actual_range byte 0, 6
attribute time_elapsed bcodmo_name String time_elapsed
attribute time_elapsed description String time since start of incubation
attribute time_elapsed long_name String Time Elapsed
attribute time_elapsed nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/ELTMZZZZ/ (external link)
attribute time_elapsed units String hours
variable cell_abund   float  
attribute cell_abund _FillValue float NaN
attribute cell_abund actual_range float 469000.0, 3790000.0
attribute cell_abund bcodmo_name String cell_concentration
attribute cell_abund description String microbial cell abundance
attribute cell_abund long_name String Cell Abund
attribute cell_abund units String cells/milliliter
variable carbon_fix   short  
attribute carbon_fix _FillValue short 32767
attribute carbon_fix actual_range short 0, 336
attribute carbon_fix bcodmo_name String unknown
attribute carbon_fix description String carbon fixation rate
attribute carbon_fix long_name String Carbon Fix
attribute carbon_fix units String microgram Carbon/liter/day
variable NOX   float  
attribute NOX _FillValue float NaN
attribute NOX actual_range float 1.07, 18.31
attribute NOX bcodmo_name String NO3_NO2
attribute NOX description String Nitrate+nitrite concentration during incubations
attribute NOX long_name String NOX
attribute NOX units String micromol/liter

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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