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Title Sum-
Institution Dataset ID
   set  data   graph     files  public 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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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 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
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).
attribute NC_GLOBAL awards_0_award_nid String 54989
attribute NC_GLOBAL awards_0_award_number String OCE-1136608
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1136608 (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 David L. Garrison
attribute NC_GLOBAL awards_0_program_manager_nid String 50534
attribute NC_GLOBAL cdm_data_type String Other
attribute NC_GLOBAL comment String Microbial incubations in diffuse flow vent fluids
D. Foustoukos

version: 2017-02-07 (added cell concentration and d15N data)
replaces version: 2015-12-17
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 date_created String 2015-12-16T19:28:02Z
attribute NC_GLOBAL date_modified String 2017-02-13T20:07:38Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.682108
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/628993 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_dataset_instrument_description String Olympus BX61 microscope with a UPlanF1 100x  (numerical aperture, 1.3) oil immersion objective
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 629004
attribute NC_GLOBAL instruments_0_description String 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".
attribute NC_GLOBAL instruments_0_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/LAB05/ (external link)
attribute NC_GLOBAL instruments_0_instrument_name String Microscope-Optical
attribute NC_GLOBAL instruments_0_instrument_nid String 708
attribute NC_GLOBAL instruments_1_dataset_instrument_description String JSM-6500F field emission scanning electron microscope (JEOL)
attribute NC_GLOBAL instruments_1_dataset_instrument_nid String 629005
attribute NC_GLOBAL instruments_1_description String Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of electrons behaving as waves.
attribute NC_GLOBAL instruments_1_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/LAB07/ (external link)
attribute NC_GLOBAL instruments_1_instrument_name String Microscope-Electron
attribute NC_GLOBAL instruments_1_instrument_nid String 709
attribute NC_GLOBAL instruments_2_acronym String IGT Sampler
attribute NC_GLOBAL instruments_2_dataset_instrument_nid String 629000
attribute NC_GLOBAL instruments_2_description String 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.
attribute NC_GLOBAL instruments_2_instrument_name String Isobaric Gas-Tight Sampler
attribute NC_GLOBAL instruments_2_instrument_nid String 529049
attribute NC_GLOBAL instruments_2_supplied_name String IGT Sampler
attribute NC_GLOBAL instruments_3_dataset_instrument_description String 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
attribute NC_GLOBAL instruments_3_dataset_instrument_nid String 629003
attribute NC_GLOBAL instruments_3_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_3_instrument_name String Shipboard Incubator
attribute NC_GLOBAL instruments_3_instrument_nid String 629001
attribute NC_GLOBAL instruments_3_supplied_name String custom high pressure bioreactor
attribute NC_GLOBAL keywords String 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
attribute NC_GLOBAL keywords_vocabulary String GCMD Science Keywords
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/628993/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/628993 (external link)
attribute NC_GLOBAL param_mapping String {'628993': {}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/628993/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String Carnegie Institution for Science
attribute NC_GLOBAL people_0_affiliation_acronym String CIS
attribute NC_GLOBAL people_0_person_name String Dionysis Foustoukos
attribute NC_GLOBAL people_0_person_nid String 51518
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 Nancy Copley
attribute NC_GLOBAL people_1_person_nid String 50396
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 Microbial Communities at Deep-Sea Vents
attribute NC_GLOBAL projects_0_acronym String Microbial Communities at Deep-Sea Vents
attribute NC_GLOBAL projects_0_description String 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)
attribute NC_GLOBAL projects_0_end_date String 2014-09
attribute NC_GLOBAL projects_0_name String An Integrated Study of Energy Metabolism, Carbon Fixation, and Colonization Mechanisms in Chemosynthetic Microbial Communities at Deep-Sea Vents
attribute NC_GLOBAL projects_0_project_nid String 2216
attribute NC_GLOBAL projects_0_start_date String 2011-10
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 subsetVariables String flow_rate
attribute NC_GLOBAL summary String 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).


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.
attribute NC_GLOBAL title String 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)
attribute NC_GLOBAL version String 2
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable description   String  
attribute description bcodmo_name String exp_id
attribute description description String description of experimental incubation
attribute description long_name String Description
attribute description units String unitless
variable date_start   String  
attribute date_start bcodmo_name String date_start
attribute date_start description String start date of incubation in yyyy-mm-dd format
attribute date_start long_name String Date Start
attribute date_start source_name String date_start
attribute date_start time_precision String 1970-01-01
attribute date_start units String unitless
variable date_end   String  
attribute date_end bcodmo_name String date_end
attribute date_end description String end date of incubation in yyyy-mm-dd format
attribute date_end long_name String Date End
attribute date_end time_precision String 1970-01-01
attribute date_end units String unitless
variable flow_rate   float  
attribute flow_rate _FillValue float NaN
attribute flow_rate actual_range float 0.042, 0.042
attribute flow_rate bcodmo_name String unknown
attribute flow_rate description String flow rate
attribute flow_rate long_name String Flow Rate
attribute flow_rate units String milliliters/minute
variable temp   byte  
attribute temp _FillValue byte 127
attribute temp actual_range byte 30, 50
attribute temp bcodmo_name String temperature
attribute temp description String temperature
attribute temp long_name String Temperature
attribute temp nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/TEMPP901/ (external link)
attribute temp units String degrees Celsius
variable press   byte  
attribute press _FillValue byte 127
attribute press actual_range byte 5, 25
attribute press bcodmo_name String pressure
attribute press description String pressure
attribute press long_name String Press
attribute press nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/PRESPR01/ (external link)
attribute press units String MegaPascals
variable time_elapsed   short  
attribute time_elapsed _FillValue short 32767
attribute time_elapsed actual_range short 0, 356
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_concentration   int  
attribute cell_concentration _FillValue int 2147483647
attribute cell_concentration actual_range int 660000, 15500000
attribute cell_concentration bcodmo_name String cell_concentration
attribute cell_concentration description String cell_concentration
attribute cell_concentration long_name String Cell Concentration
attribute cell_concentration units String unknown
variable NO3_uM   float  
attribute NO3_uM _FillValue float NaN
attribute NO3_uM actual_range float 3.3, 1568.0
attribute NO3_uM bcodmo_name String NO3
attribute NO3_uM colorBarMaximum double 50.0
attribute NO3_uM colorBarMinimum double 0.0
attribute NO3_uM description String nitrate concentration
attribute NO3_uM long_name String Mole Concentration Of Nitrate In Sea Water
attribute NO3_uM nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/NTRAIGGS/ (external link)
attribute NO3_uM units String umoles/kgr
variable NH4_uM   float  
attribute NH4_uM _FillValue float NaN
attribute NH4_uM actual_range float 1.4, 248.0
attribute NH4_uM bcodmo_name String Ammonium
attribute NH4_uM colorBarMaximum double 5.0
attribute NH4_uM colorBarMinimum double 0.0
attribute NH4_uM description String ammonium concentration
attribute NH4_uM long_name String Mole Concentration Of Ammonium In Sea Water
attribute NH4_uM nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/AMONAAZX/ (external link)
attribute NH4_uM units String umoles/kgr
variable H2_uM   float  
attribute H2_uM _FillValue float NaN
attribute H2_uM actual_range float 0.01, 122.0
attribute H2_uM bcodmo_name String unknown
attribute H2_uM description String hydrogen concentration
attribute H2_uM long_name String H2 U M
attribute H2_uM units String umoles/kgr
variable H2S_uM   float  
attribute H2S_uM _FillValue float NaN
attribute H2S_uM actual_range float 0.13, 666.0
attribute H2S_uM bcodmo_name String sulfide
attribute H2S_uM description String hydrogen sulfide concentration
attribute H2S_uM long_name String H2 S U M
attribute H2S_uM units String umoles/kgr
variable CH4_uM   float  
attribute CH4_uM _FillValue float NaN
attribute CH4_uM actual_range float 3.8, 14.4
attribute CH4_uM bcodmo_name String unknown
attribute CH4_uM description String methane concentration
attribute CH4_uM long_name String CH4 U M
attribute CH4_uM units String umoles/kgr
variable pH   float  
attribute pH _FillValue float NaN
attribute pH actual_range float 5.5, 7.1
attribute pH bcodmo_name String pH
attribute pH colorBarMaximum double 9.0
attribute pH colorBarMinimum double 7.0
attribute pH description String pH at 25 C
attribute pH long_name String Sea Water Ph Reported On Total Scale
attribute pH nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/PHXXZZXX/ (external link)
attribute pH units String unitless
variable d15N_NO3_ppt   float  
attribute d15N_NO3_ppt _FillValue float NaN
attribute d15N_NO3_ppt actual_range float -6.5, 11.8
attribute d15N_NO3_ppt bcodmo_name String d15N
attribute d15N_NO3_ppt colorBarMaximum double 50.0
attribute d15N_NO3_ppt colorBarMinimum double 0.0
attribute d15N_NO3_ppt description String d15N_NO3_ppt
attribute d15N_NO3_ppt long_name String Mole Concentration Of Nitrate In Sea Water
attribute d15N_NO3_ppt units String unknown
variable d15N_Biomass_ppt   float  
attribute d15N_Biomass_ppt _FillValue float NaN
attribute d15N_Biomass_ppt actual_range float -0.6, -0.5
attribute d15N_Biomass_ppt bcodmo_name String d15N
attribute d15N_Biomass_ppt description String d15N_Biomass_ppt
attribute d15N_Biomass_ppt long_name String D15 N Biomass Ppt
attribute d15N_Biomass_ppt units String unknown

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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