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Dataset Title:  Results from shipboard high-pressure incubations of diffuse flow vent fluids
collected from the Crab Spa and Alvinella sites at East Pacific Rise during the
AT26-10 expedition, Jan. 2014 (Microbial Communities at Deep-Sea Vents project)
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Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_628993)
Information:  Summary ? | License ? | ISO 19115 | Metadata | Background (external link) | Subset | Data Access Form | Files
 
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The Dataset Attribute Structure (.das) for this Dataset

Attributes {
 s {
  description {
    String bcodmo_name "exp_id";
    String description "description of experimental incubation";
    String long_name "Description";
    String units "unitless";
  }
  date_start {
    String bcodmo_name "date_start";
    String description "start date of incubation in yyyy-mm-dd format";
    String long_name "Date Start";
    String source_name "date_start";
    String time_precision "1970-01-01";
    String units "unitless";
  }
  date_end {
    String bcodmo_name "date_end";
    String description "end date of incubation in yyyy-mm-dd format";
    String long_name "Date End";
    String time_precision "1970-01-01";
    String units "unitless";
  }
  flow_rate {
    Float32 _FillValue NaN;
    Float32 actual_range 0.042, 0.042;
    String bcodmo_name "unknown";
    String description "flow rate";
    String long_name "Flow Rate";
    String units "milliliters/minute";
  }
  temp {
    Byte _FillValue 127;
    Byte actual_range 30, 50;
    String bcodmo_name "temperature";
    String description "temperature";
    String long_name "Temperature";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/TEMPP901/";
    String units "degrees Celsius";
  }
  press {
    Byte _FillValue 127;
    Byte actual_range 5, 25;
    String bcodmo_name "pressure";
    String description "pressure";
    String long_name "Press";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/PRESPR01/";
    String units "MegaPascals";
  }
  time_elapsed {
    Int16 _FillValue 32767;
    Int16 actual_range 0, 356;
    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_concentration {
    Int32 _FillValue 2147483647;
    Int32 actual_range 660000, 15500000;
    String bcodmo_name "cell_concentration";
    String description "cell_concentration";
    String long_name "Cell Concentration";
    String units "unknown";
  }
  NO3_uM {
    Float32 _FillValue NaN;
    Float32 actual_range 3.3, 1568.0;
    String bcodmo_name "NO3";
    Float64 colorBarMaximum 50.0;
    Float64 colorBarMinimum 0.0;
    String description "nitrate concentration";
    String long_name "Mole Concentration Of Nitrate In Sea Water";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/NTRAIGGS/";
    String units "umoles/kgr";
  }
  NH4_uM {
    Float32 _FillValue NaN;
    Float32 actual_range 1.4, 248.0;
    String bcodmo_name "Ammonium";
    Float64 colorBarMaximum 5.0;
    Float64 colorBarMinimum 0.0;
    String description "ammonium concentration";
    String long_name "Mole Concentration Of Ammonium In Sea Water";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/AMONAAZX/";
    String units "umoles/kgr";
  }
  H2_uM {
    Float32 _FillValue NaN;
    Float32 actual_range 0.01, 122.0;
    String bcodmo_name "unknown";
    String description "hydrogen concentration";
    String long_name "H2 U M";
    String units "umoles/kgr";
  }
  H2S_uM {
    Float32 _FillValue NaN;
    Float32 actual_range 0.13, 666.0;
    String bcodmo_name "sulfide";
    String description "hydrogen sulfide concentration";
    String long_name "H2 S U M";
    String units "umoles/kgr";
  }
  CH4_uM {
    Float32 _FillValue NaN;
    Float32 actual_range 3.8, 14.4;
    String bcodmo_name "unknown";
    String description "methane concentration";
    String long_name "CH4 U M";
    String units "umoles/kgr";
  }
  pH {
    Float32 _FillValue NaN;
    Float32 actual_range 5.5, 7.1;
    String bcodmo_name "pH";
    Float64 colorBarMaximum 9.0;
    Float64 colorBarMinimum 7.0;
    String description "pH at 25 C";
    String long_name "Sea Water Ph Reported On Total Scale";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/PHXXZZXX/";
    String units "unitless";
  }
  d15N_NO3_ppt {
    Float32 _FillValue NaN;
    Float32 actual_range -6.5, 11.8;
    String bcodmo_name "d15N";
    Float64 colorBarMaximum 50.0;
    Float64 colorBarMinimum 0.0;
    String description "d15N_NO3_ppt";
    String long_name "Mole Concentration Of Nitrate In Sea Water";
    String units "unknown";
  }
  d15N_Biomass_ppt {
    Float32 _FillValue NaN;
    Float32 actual_range -0.6, -0.5;
    String bcodmo_name "d15N";
    String description "d15N_Biomass_ppt";
    String long_name "D15 N Biomass Ppt";
    String units "unknown";
  }
 }
  NC_GLOBAL {
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
    String acquisition_description 
"From AT26-10\\u00a0cruise report (01/29/2014):  
DOB: An Integrated Study of Energy Metabolism, Carbon Fixation, and
Colonization Mechanisms in Chemosynthetic Microbial Communities at Deep-Sea
Vents  
 Cruise Report by the CIW research team: Dr. Ileana Perez-Rodriguez, Mr. Matt
Rawls and Dr. Dionysis I. Foustoukos  
 The CIW team was responsible for the shipboard continuous culturing
incubations of vent fluids collected from Crab Spa and Tica hot springs during
the AT26-10 expedition at 9oN EPR by utilizing our high-pressure bioreactor
(Fig. 1). This was accomplished through a collaborative effort with Jeff
Seewald and Sean Sylva (WHOI), who deployed isobaric gas-tight samplers (IGTs)
to collect hydrothermal vent fluids at the diffuse flow sites. Experiments
were designed to study the cycling to N through the metabolic processes of
denitrification and dissimilatory nitrate reduction to ammonia (DNRA) under
in-situ deep-sea vent temperature and pressure conditions.
 
We studied the evolution of nitrate reducing microorganisms at mesophilic
(30oC) and thermophilic (50oC) conditions at pressures ranging from 5 to 250
bar. Vent fluids (16 IGTs) were delivered in the bioreactor and homogeneously
mixed with aqueous media solution enriched in dissolved nitrate, hydrogen and
13C labeled bicarbonate to facilitate the growth of nitrate reducing
microorganisms (Fig. 2). The two distinct sets of experiments were lasted for
356 and 100 hours. In short, experimental results constrained the function and
metabolic rates of the denitrifying microbial communities in the Crab Spa
fluids, while DNRA metabolic pathways were identified for the populations
residing in the moderate temperature vent fluids (60oC) of the Alvinella
colony at Tica.
 
During the course of the experiments we monitored the growth of deep-sea
microbial communities by measuring the concentrations of dissolved aqueous
species directly involved in nitrate based metabolism, such as NO3, NH4, H2
and H2S. We also monitored cell densities by utilizing an epi-fluorescence
microscope (Sievert, WHOI). Dissolved gas and NH4+ concentrations were
attained by gas and ion chromatography (Seewald - Sylva, WHOI). Subsamples
were also collected for a number of offshore analysis to determine: i) the
15N/14N isotope composition of NO3-,/NH4+ and constrain kinetic isotope
effects associated with denitrification/DNRA (Perez-Rodriguez, CIW), ii) to
study the rates of autotrophic carbon fixation by NanoSIMS (Musat, UFZ), iii)
to perform single cell genomics on the microbial populations grown in the
bioreactor (Ramunas, Bigelow) and (iv) to isolate and characterize novel
microogranisms from the communities cultured in our experiments (Perez-
Rodriguez, CIW and Vetriani, Rutgers).";
    String awards_0_award_nid "54989";
    String awards_0_award_number "OCE-1136608";
    String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1136608";
    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 "David L. Garrison";
    String awards_0_program_manager_nid "50534";
    String cdm_data_type "Other";
    String comment 
"Microbial incubations in diffuse flow vent fluids 
   D. Foustoukos 
  
   version: 2017-02-07 (added cell concentration and d15N data) 
      replaces version: 2015-12-17";
    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 date_created "2015-12-16T19:28:02Z";
    String date_modified "2017-02-13T20:07:38Z";
    String defaultDataQuery "&time<now";
    String doi "10.1575/1912/bco-dmo.682108";
    String history 
"2022-10-05T21:22:55Z (local files)
2022-10-05T21:22:55Z https://erddap.bco-dmo.org/tabledap/bcodmo_dataset_628993.das";
    String infoUrl "https://www.bco-dmo.org/dataset/628993";
    String institution "BCO-DMO";
    String instruments_0_dataset_instrument_description "Olympus BX61 microscope with a UPlanF1 100x  (numerical aperture, 1.3) oil immersion objective";
    String instruments_0_dataset_instrument_nid "629004";
    String instruments_0_description "Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of visible light. Includes conventional and inverted instruments. Also called a \"light microscope\".";
    String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB05/";
    String instruments_0_instrument_name "Microscope-Optical";
    String instruments_0_instrument_nid "708";
    String instruments_1_dataset_instrument_description "JSM-6500F field emission scanning electron microscope (JEOL)";
    String instruments_1_dataset_instrument_nid "629005";
    String instruments_1_description "Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of electrons behaving as waves.";
    String instruments_1_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB07/";
    String instruments_1_instrument_name "Microscope-Electron";
    String instruments_1_instrument_nid "709";
    String instruments_2_acronym "IGT Sampler";
    String instruments_2_dataset_instrument_nid "629000";
    String instruments_2_description "Isobaric Gas Tight (IGT) samplers, designed and built by scientists and engineers at WHOI, are titanium instruments designed to be used with deep submergence vehicles to sample corrosive hydrothermal vent fluids at high temperature and high pressure. The IGT prevents the sampled fluid from degassing as pressure decreases during the vehicle’s ascent to the surface.";
    String instruments_2_instrument_name "Isobaric Gas-Tight Sampler";
    String instruments_2_instrument_nid "529049";
    String instruments_2_supplied_name "IGT Sampler";
    String instruments_3_dataset_instrument_description "The integrated system allows for the culturing of microorganisms under hydrostatic pressures from 0.1 to 69 MPa (and up to 138 MPa with ongoing developments) and at temperatures ranging from 25 to 120°C. For full description, see Foustoukos and Perez-Rodriguez (2015), Applied and Environmental Microbiology, 81, 6850";
    String instruments_3_dataset_instrument_nid "629003";
    String instruments_3_description "A device mounted on a ship that holds water samples under conditions of controlled temperature or controlled temperature and illumination.";
    String instruments_3_instrument_name "Shipboard Incubator";
    String instruments_3_instrument_nid "629001";
    String instruments_3_supplied_name "custom high pressure bioreactor";
    String keywords "ammonia, ammonium, bco, bco-dmo, biological, biomass, cell, cell_concentration, ch4, CH4_uM, chemical, chemistry, concentration, d15, d15N_Biomass_ppt, d15N_NO3_ppt, data, dataset, date, date_end, description, dmo, earth, Earth Science > Oceans > Ocean Chemistry > Ammonia, Earth Science > Oceans > Ocean Chemistry > Nitrate, Earth Science > Oceans > Ocean Chemistry > pH, elapsed, end, erddap, flow, flow_rate, H2_uM, H2S_uM, management, mole, mole_concentration_of_ammonium_in_sea_water, mole_concentration_of_nitrate_in_sea_water, n02, nh4, NH4_uM, nitrate, no3, NO3_uM, ocean, oceanography, oceans, office, ppt, preliminary, press, rate, reported, scale, science, sea, sea_water_ph_reported_on_total_scale, seawater, start, temperature, time, time_elapsed, total, u, water";
    String keywords_vocabulary "GCMD Science Keywords";
    String license "https://www.bco-dmo.org/dataset/628993/license";
    String metadata_source "https://www.bco-dmo.org/api/dataset/628993";
    String param_mapping "{'628993': {}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/628993/parameters";
    String people_0_affiliation "Carnegie Institution for Science";
    String people_0_affiliation_acronym "CIS";
    String people_0_person_name "Dionysis Foustoukos";
    String people_0_person_nid "51518";
    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 "Nancy Copley";
    String people_1_person_nid "50396";
    String people_1_role "BCO-DMO Data Manager";
    String people_1_role_type "related";
    String project "Microbial Communities at Deep-Sea Vents";
    String projects_0_acronym "Microbial Communities at Deep-Sea Vents";
    String projects_0_description 
"Deep-sea hydrothermal vents, first discovered in 1977, are poster child ecosystems where microbial chemosynthesis rather than photosynthesis is the primary source of organic carbon. Significant gaps remain in our understanding of the underlying microbiology and biogeochemistry of these fascinating ecosystems. Missing are the identification of specific microorganisms mediating critical reactions in various geothermal systems, metabolic pathways used by the microbes, rates of the catalyzed reactions, amounts of organic carbon being produced, and the larger role of these ecosystems in global biogeochemical cycles. To fill these gaps, the investigators will conduct a 3-year interdisciplinary, international hypothesis-driven research program to understand microbial processes and their quantitative importance at deep-sea vents. Specifically, the investigators will address the following objectives:  1. Determine key relationships between the taxonomic, genetic and functional diversity, as well as the mechanisms of energy and carbon transfer, in deep-sea hydrothermal vent microbial communities.  2. Identify the predominant metabolic pathways and thus the main energy sources driving chemoautotrophic production in high and low temperature diffuse flow vents.  3. Determine energy conservation efficiency and rates of aerobic and anaerobic chemosynthetic primary productivity in high and low temperature diffuse flow vents.  4. Determine gene expression patterns in diffuse-flow vent microbial communities during attachment to substrates and the development of biofilms.


Integration: To address these objectives and to characterize the complexity of microbially-catalyzed processes at deep-sea vents at a qualitatively new level, we will pursue an integrated approach that couples an assessment of taxonomic diversity using cultivation-dependent and -independent approaches with methodologies that address genetic diversity, including a) metagenomics (genetic potential and diversity of community), b) single cell genomics (genetic potential and diversity of uncultured single cells), c) meta-transcriptomics and -proteomics (identification and function of active community members, realized potential of the community). To assess function and response to the environment, these approaches will be combined with 1) measurement of in situ rates of chemoautotrophic production, 2) geochemical characterization of microbial habitats, and 3) shipboard incubations under simulated in situ conditions (hypothesis testing under controlled physicochemical conditions). Network approaches and mathematical simulation will be used to reconstruct the metabolic network of the natural communities. A 3-day long project meeting towards the end of the second year will take place in Woods Hole. This Data Integration and Synthesis meeting will allow for progress reports and presentations from each PI, postdoc, and/or student, with the aim of synthesizing data generated to facilitate the preparation of manuscripts.


Intellectual Merit. Combining the community expression profile with diversity and metagenomic analyses as well as process and habitat characterization will be unique to hydrothermal vent microbiology. The approach will provide new insights into the functioning of deep-sea vent microbial communities and the constraints regulating the interactions between the microbes and their abiotic and biotic environment, ultimately enabling us to put these systems into a quantitative framework and thus a larger global context.


Broader Impacts. This is an interdisciplinary and collaborative effort between 4 US and 4 foreign institutions, creating unique opportunities for networking and fostering international collaborations. This will also benefit the involved students (2 graduate, several undergraduate) and 2 postdoctoral associates. This project will directly contribute to many educational and public outreach activities of the involved PIs, including the WHOI Dive & Discover program; single cell genomics workshops and Cafe Scientifique (Bigelow); REU (WHOI, Bigelow, CIW); COSEE and RIOS (Rutgers), and others. The proposed research fits with the focus of a number of multidisciplinary and international initiatives, in which PIs are active members (SCOR working group on Hydrothermal energy and the ocean carbon cycle, http://www.scorint. org/Working_Groups/wg135.htm; Deep Carbon Observatory at CIW, https://dco.gl.ciw.edu/; Global Biogeochemical Flux (GBF) component of the Ocean Observatories Initiative (OOI), https://www.whoi.edu/GBF-OOI/page.do?pid=41475)";
    String projects_0_end_date "2014-09";
    String projects_0_name "An Integrated Study of Energy Metabolism, Carbon Fixation, and Colonization Mechanisms in Chemosynthetic Microbial Communities at Deep-Sea Vents";
    String projects_0_project_nid "2216";
    String projects_0_start_date "2011-10";
    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 subsetVariables "flow_rate";
    String summary 
"This dataset includes results from shipboard high-pressure incubations of
diffuse flow vent fluids collected from the Crab Spa (9.8398\\u00ba N,
104.2913\\u00ba W) and Alvinella (9.8398\\u00ba N, 104.2915\\u00ba W) sites at
East Pacific Rise during the AT26-10 oceanographic expedition in January 2014.
Reported parameters include dates and time elapsed, flow rate, temperature,
pressure, and pH, and concentrations of NO3, NH4, H2, H2S, CH4.
 
Vent fluids used in shipboard incubations were corrected from diffuse flow
vent sites at the East Pacific Rise (2503 m): Crab Spa (9.8398\\u00ba N,
104.2913\\u00ba W) and Alvinella (9.8398\\u00ba N, 104.2915\\u00ba W) (see
description in McNichol et al. [2016]). Fluids were collected using isobaric
gas-tight samplers [Seewald et al., 2002] prior to their transfer to the
shipboard continuous culture system [Foustoukos and Perez-Rodriguez, 2015].
Here, high-pressure incubations (250 bars) were conducted at mesophilic (30
\\u00baC) and thermophilic (50 \\u00baC) conditions to constrain the function
and metabolic rates of denitrifying and DNRA microbial communities residing at
Crab Spa and Alvinella, respectively. To enhance the activity of nitrate-
respiring anaerobic bacteria, an NO3- (5 mm) and H2(aq) (1.30 mM)-enriched
medium was introduced in the high-pressure incubations under strictly
anaerobic conditions. Dissolved HCO3- (7.3 mm, 13C labeled) was used as added
carbon source. Vent fluids were introduced at a flow rate of 0.042 mL/min,
while growth medium was added at a rate of 0.0042 mL/min. The two sets of
experiments were performed for 356 (Crab Spa) and 50 hours (Alvinella). Direct
cell counts were conducted by staining cells with 0.1% acridine orange and
counting them with a fluorescence microscope. 15N/14N isotopic analysis of the
NO3-, NH4+ and biomass were conducted with a Thermo Scientific Delta VPlus
mass spectrometer and CE Instruments NA 2500 series elemental analyzer (EA).
 
References:
 
Foustoukos, D., and I. Perez-Rodriguez (2015), A continuous culture system for
assessing microbial activities in the piezosphere, Applied and Environmental
Microbiology, 81(19), 6850-6856.
 
McNichol, J., S. P. Sylva, F. Thomas, C. D. Taylor, S. M. Sievert, and J. S.
Seewald (2016), Assessing microbial processes in deep-sea hydrothermal systems
by incubation at in situ temperature and pressure, Deep Sea Research Part I:
Oceanographic Research Papers, 115, 221-232.
 
Seewald, J. S., K. W. Doherty, T. R. Hammar, and S. P. Liberatore (2002), A
new gas-tight isobaric sampler for hydrothermal fluids, Deep-Sea Research,
Part I: Oceanographic Research Papers, 49(1), 189-196.";
    String title "Results from shipboard high-pressure incubations of diffuse flow vent fluids collected from the Crab Spa and Alvinella sites at East Pacific Rise during the AT26-10 expedition, Jan. 2014 (Microbial Communities at Deep-Sea Vents project)";
    String version "2";
    String xml_source "osprey2erddap.update_xml() v1.3";
  }
}

 

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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