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Dataset Title:  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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Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_788911)
Information:  Summary ? | License ? | ISO 19115 | Metadata | Background (external link) | Data Access Form | Files
 
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The Dataset Attribute Structure (.das) for this Dataset

Attributes {
 s {
  incubation {
    Byte _FillValue 127;
    Byte actual_range 1, 6;
    String bcodmo_name "sample";
    String description "incubation run identifier";
    String long_name "Incubation";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
    String units "unitless";
  }
  time_elapsed {
    Byte _FillValue 127;
    Byte actual_range 0, 6;
    String bcodmo_name "time_elapsed";
    String description "time since start of incubation";
    String long_name "Time Elapsed";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ELTMZZZZ/";
    String units "hours";
  }
  cell_abund {
    Float32 _FillValue NaN;
    Float32 actual_range 469000.0, 3790000.0;
    String bcodmo_name "cell_concentration";
    String description "microbial cell abundance";
    String long_name "Cell Abund";
    String units "cells/milliliter";
  }
  carbon_fix {
    Int16 _FillValue 32767;
    Int16 actual_range 0, 336;
    String bcodmo_name "unknown";
    String description "carbon fixation rate";
    String long_name "Carbon Fix";
    String units "microgram Carbon/liter/day";
  }
  NOX {
    Float32 _FillValue NaN;
    Float32 actual_range 1.07, 18.31;
    String bcodmo_name "NO3_NO2";
    String description "Nitrate+nitrite concentration during incubations";
    String long_name "NOX";
    String units "micromol/liter";
  }
 }
  NC_GLOBAL {
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
    String acquisition_description 
"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
25(+/-2)\\u02daC.
 
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
production.
 
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.";
    String awards_0_award_nid "685772";
    String awards_0_award_number "OCE-1559198";
    String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1559198";
    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 awards_1_award_nid "685780";
    String awards_1_award_number "OCE-1559042";
    String awards_1_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1559042";
    String awards_1_funder_name "NSF Division of Ocean Sciences";
    String awards_1_funding_acronym "NSF OCE";
    String awards_1_funding_source_nid "355";
    String awards_1_program_manager "Michael E. Sieracki";
    String awards_1_program_manager_nid "50446";
    String cdm_data_type "Other";
    String comment 
"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";
    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 "2020-01-30T14:33:34Z";
    String date_modified "2020-07-02T19:28:18Z";
    String defaultDataQuery "&time<now";
    String doi "10.26008/1912/bco-dmo.788911.1";
    String history 
"2020-09-25T17:59:17Z (local files)
2020-09-25T17:59:17Z https://erddap.bco-dmo.org/tabledap/bcodmo_dataset_788911.das";
    String infoUrl "https://www.bco-dmo.org/dataset/788911";
    String institution "BCO-DMO";
    String instruments_0_acronym "IR Mass Spec";
    String instruments_0_dataset_instrument_description "Used for carbon fixation measurements.";
    String instruments_0_dataset_instrument_nid "788944";
    String instruments_0_description "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).";
    String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB16/";
    String instruments_0_instrument_name "Isotope-ratio Mass Spectrometer";
    String instruments_0_instrument_nid "469";
    String instruments_0_supplied_name "DeltaPlus Isotope Ratio Mass Spectrometer  with attached Finnigan-MAT Conflo-II interface";
    String instruments_1_dataset_instrument_description "Used for microbial cell counts.";
    String instruments_1_dataset_instrument_nid "788945";
    String instruments_1_description "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.";
    String instruments_1_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB06/";
    String instruments_1_instrument_name "Microscope-Fluorescence";
    String instruments_1_instrument_nid "695";
    String instruments_2_dataset_instrument_description "Used for carbon fixation measurements";
    String instruments_2_dataset_instrument_nid "788943";
    String instruments_2_description "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.";
    String instruments_2_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB01/";
    String instruments_2_instrument_name "Elemental Analyzer";
    String instruments_2_instrument_nid "546339";
    String instruments_2_supplied_name "•	Fisons 1108 Elemental Analyzer equipped with a Costech \"Zero Blank\" sample carousel";
    String instruments_3_dataset_instrument_description "Used to generate chromatographs from the photodetector and thus measure nitrate concentrations.";
    String instruments_3_dataset_instrument_nid "806816";
    String instruments_3_description "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.";
    String instruments_3_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB01/";
    String instruments_3_instrument_name "Elemental Analyzer";
    String instruments_3_instrument_nid "546339";
    String instruments_3_supplied_name "Teledyne T200 NOx analyzer with a SRI Model 333 Peak Simple Chromatography Data System";
    String instruments_4_dataset_instrument_description "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/.";
    String instruments_4_dataset_instrument_nid "788942";
    String instruments_4_description "A device mounted on a ship that holds water samples under conditions of controlled temperature or controlled temperature and illumination.";
    String instruments_4_instrument_name "Shipboard Incubator";
    String instruments_4_instrument_nid "629001";
    String instruments_4_supplied_name "Vent-SID";
    String keywords "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";
    String license "https://www.bco-dmo.org/dataset/788911/license";
    String metadata_source "https://www.bco-dmo.org/api/dataset/788911";
    String param_mapping "{'788911': {}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/788911/parameters";
    String people_0_affiliation "Woods Hole Oceanographic Institution";
    String people_0_affiliation_acronym "WHOI";
    String people_0_person_name "Stefan M Sievert";
    String people_0_person_nid "51416";
    String people_0_role "Principal Investigator";
    String people_0_role_type "originator";
    String people_1_affiliation "University of Maine";
    String people_1_person_name "Dr Jeremy Rich";
    String people_1_person_nid "685778";
    String people_1_role "Co-Principal Investigator";
    String people_1_role_type "originator";
    String people_2_affiliation "Woods Hole Oceanographic Institution";
    String people_2_affiliation_acronym "WHOI BCO-DMO";
    String people_2_person_name "Nancy Copley";
    String people_2_person_nid "50396";
    String people_2_role "BCO-DMO Data Manager";
    String people_2_role_type "related";
    String project "vent O2 NO3 roles";
    String projects_0_acronym "vent O2 NO3 roles";
    String projects_0_description 
"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.";
    String projects_0_end_date "2019-04";
    String projects_0_geolocation "Deep-Sea hydrothermal vent field at 9 deg N on the East Pacific Rise";
    String projects_0_name "Collaborative Research: Environmental Drivers of Chemoautotrophic Carbon Production at Deep-Sea Hydrothermal Vents - Comparative Roles of Oxygen and Nitrate";
    String projects_0_project_nid "685773";
    String projects_0_start_date "2016-05";
    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 "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.";
    String title "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";
    String version "1";
    String xml_source "osprey2erddap.update_xml() v1.5";
  }
}

 

Using tabledap to Request Data and Graphs from Tabular Datasets

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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