http://lod.bco-dmo.org/id/dataset/660489
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2016-10-04
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
SSU rRNA gene sequences from marine sediments, marine subseafloor, and deep seawater sampled from the Juan de Fuca Ridge Flank from various R/V Atlantis cruises from 2008-2011 (microJdFR project)
2016-10-07
publication
2016-10-07
revision
BCO-DMO Linked Data URI
2016-10-07
creation
http://lod.bco-dmo.org/id/dataset/660489
Michael S. Rappé
University of Hawaiʻi at Mānoa
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Rappé, M. S. (2016) SSU rRNA gene sequences from marine sediments, marine subseafloor, and deep seawater sampled from the Juan de Fuca Ridge Flank from various R/V Atlantis cruises from 2008-2011 (microJdFR project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2016-10-07 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/660489 [access date]
SSU rRNA gene sequences from marine sediments, marine subseafloor, and deep seawater Dataset Description: <p>This dataset includes SSU rRNA gene sequence accession identifiers&nbsp;from marine sediments, marine subseafloor, and deep seawater along with quantities of various elements&nbsp;and&nbsp;compounds including&nbsp;(oxygen, ammonium, methane, hydrogen, total dissolved nitrogen, calcium, nitrate, nitrate, and total iron). &nbsp;Also included in this dataset are microbial cell abundance, pH, latitude and longitude. &nbsp;The sampling area in Northeast Pacific Ocean waters&nbsp;include&nbsp;long-term borehole observatories (CORKs) in the&nbsp;Juan de Fuca (JdF) Ridge Flank region from R/V Atlantis cruises AT15-35, AT15-55, AT15-66 and AT18-07..</p>
<p><strong>These data have been published in the following references:</strong></p>
<p>Jungbluth, Sean P., et al. "Data report: microbial diversity in sediment near Grizzly Bare Seamount in Holes U1363B and U1363G."&nbsp;<em>Proc. IODP&nbsp;Volume</em>. Vol. 327. 2013.&nbsp;<a href="http://dx.doi.org/10.2204/iodp.proc.327.201.2013">http://dx.doi.org/10.2204/iodp.proc.327.201.2013</a></p>
<p>Jungbluth, Sean P., et al. "Novel microbial assemblages inhabiting crustal fluids within mid-ocean ridge flank subsurface basalt."&nbsp;<em>The ISME journal&nbsp;</em>(2016).&nbsp;<a href="http://dx.doi.org/10.1038/ismej.2015.248">dx.doi.org/10.1038/ismej.2015.248</a></p>
<p>Lin, H-T, Hsieh, C-C, Cowen, JP,&nbsp;Rappe, MS (2015). Data report: dissolved and particulate organic carbon in the deep sediments of IODP Site U1363 near Grizzly Bare seamount.&nbsp;<em>Proceedings of the Integrated Ocean Drilling Program&nbsp;</em>327: 1-16. &nbsp;<a href="http://dx.doi.org/10.2204/iodp.proc.327.202.2015">dx.doi.org/10.2204/iodp.proc.327.202.2015</a></p> Methods and Sampling: <p><strong>Sampling Methodology:</strong></p>
<p>Sediment coring was performed by the IODP (described in Expedition 327 Scientists, 2011; <em>Integrated Ocean Drilling Program</em>). SSU rRNA genes were obtained as described in Jungbluth et al., 2013; <em>Proceedings of the Integrated Ocean Drilling Program</em> (see <a href="http://www.nature.com/ismej/journal/v7/n1/extref/ismej201273x7.doc">Supplementary Information Document</a>(.DOC)&nbsp;for this publication).</p>
<p>CORK borehole fluids were sampled using a custom-built water sampler (described in Cowen et al., 2012). For a detailed description of the pump system&nbsp;see&nbsp;<a href="http://dx.doi.org/10.1016/j.gca.2012.02.017">Lin, et al. 2012</a>.</p>
<p><strong>Pore water&nbsp;dissolved organic carbon (</strong>from&nbsp;Lin et al., 2015<em>&nbsp;</em><a href="http://publications.iodp.org/proceedings/327/202/202_3.htm">Materials and Methods&nbsp;</a>).</p>
<p>Sedimentary pore water DOC concentrations were measured by high-temperature combustion using a Shimadzu TOC-VCSH analyzer. The combustion temperature was set at 720C to ensure complete oxidation of organic matter. Samples were acidified to pH &lt;2 by the addition of 45 uL of 2 M HCl to 3 mL samples. No acid contamination was observed based on monitoring the DOC value of low-carbon deionized water. Samples were purged with nitrogen gas within the autosampler syringe for 2 min in order to remove inorganic carbon. An injection volume of 150 uL was used, with five or six injections per sample. The reproducibility between replicate injections was &lt;1 uM. Analytical reference materials (ARM) supplied by Dr. Dennis Hansell (RSMAS, University of Miami) were measured before, between, and after analysis of environmental samples (Sharp et al., 2002; Dickson et al., 2007). At least one ARM was measured every five samples. The average measured concentration of the ARM was 42 plus or minus 2 uM (n&nbsp;= 44); the reported value was 41–43 uM. Our detection limit for DOC concentrations was ~2 uM.</p>
<p><strong>Sediment organic carbon and nitrogen &nbsp;(</strong>relevant text extracted from&nbsp;Lin et al., 2015<em>&nbsp;</em><a href="http://publications.iodp.org/proceedings/327/202/202_3.htm">Materials and Methods&nbsp;</a>).</p>
<p>Whole sediment samples were analyzed for concentration of total carbon, organic carbon, and total nitrogen using an elemental combustion system (Costech ECS 4010) connected inline to an isotope-ratio mass spectrometer (Thermo Finnigan Delta XP). The amount of powdered sediment used for the analyses was optimized to provide sufficient carbon and nitrogen for isotopic composition analysis and varied between 26 and 425 mg. A subset of samples was acidified by fuming with concentrated HCl (Hedges and Stern, 1984) in order to remove inorganic carbon and quantify the particulate organic carbon (POC) content. Acid fuming did not remove inorganic nitrogen, resulting in insignificant differences between whole and acid-fumed total particulate nitrogen (PN) concentrations.</p>
<p><strong>Analytical methods for&nbsp;geochemistry </strong></p>
<p>Text below extracted from <a href="http://www.nature.com/ismej/journal/v10/n8/extref/ismej2015248x1.pdf">Supplementary Information</a> (PDF)&nbsp;Junbluth et al., 2016. &nbsp;See reference for full description.</p>
<p>Major ions (Ca2+, Mg2+, K+ , Na+, Cl- , SO4 2- and Br- ) were analyzed by ion chromatography on a Dionex ICS-1100s (Sunnyvale, CA, USA). In addition, magnesium and calcium concentrations were also analyzed by EDTA (colorimetric) and EGTA (electrometric) titration (Grasshoff et al., 1999), or inductively coupled plasma optical emission spectroscopy (ICP-OES) (Lin et al., 2012).&nbsp;</p>
<p>Silicate, nitrate, nitrite, phosphate, dissolved sulfide and dissolved manganese concentrations were measured by colorimetry (Brewer and Spencer, 1971; Phillips et al., 1997; Grasshoff et al., 1999).&nbsp;</p>
<p>&nbsp;Ammonium concentrations were measured by a flow injection-fluorometric method (Jones, 1991). The detection limit was ~2 µM for ammonium in basement fluids and the analytical uncertainty is 0.5 µM.</p>
<p>Ferrous iron was measured directly by a Ferrozine colorimetry method (Stookey, 1970; Gibbs, 1976).</p>
<p>For total iron analysis, samples were first reduced with ascorbic acid and analyzed as ferrous iron. The detection limit for both ferrous iron and total iron was 0.1 µM.</p>
<p>Dissolved organic carbon (DOC) was measured by high-temperature combustion using a TOC-VCSH analyzer (Sharp et al., 2002a; Dickson et al., 2007) (Shimadzu Corp., Kyoto, Japan).&nbsp;</p>
<p>Total dissolved nitrogen (TDN) was measured with a chemiluminescence detector in-line with a Shimadzu TOC-VCSH analyzer (Sharp et al., 2002b).</p>
<p>Alkalinity was determined by acid titration. Acid (0.1N HCl) was standardized with CO2 certified reference materials (CRMs) purchased from the office of Andrew Dickson at Scripps Institution of Oceanography.&nbsp;</p>
<p>An Orion 911600 Semi-micro pH electrode (ThermoFisher Scientific, Waltham, MA, USA) was used to measure the pH and electrode potential during the titration process. The Gran function plot method was used to evaluate titration end-points and calculate sample alkalinity (Dickson et al., 2007). The analytical reproducibility for alkalinity measurements was &lt;0.02 mM.</p>
<p><strong>SSU rRNA gene cloning and sequencing&nbsp;</strong>(from&nbsp;<a href="http://www.nature.com/ismej/journal/v7/n1/extref/ismej201273x7.doc">Supplementary Information Document</a>(DOC)&nbsp;for Junbluth et al., 2013).</p>
<p>Small subunit ribosomal RNA (SSU rRNA) gene fragments were amplified via the polymerase chain reaction (PCR) using the universal oligonucleotide forward and reverse primers 519F (5’-CAGCMGCCGCGGTAATWC-3’) and 1406R (5’-ACGGGCGGTGTGTRC-3’), respectively. Each 20 ul PCR reaction contained 0.25 U of PicoMaxx high fidelity DNA polymerase (Stratagene, La Jolla, CA), 1x PicoMaxx reaction buffer, 200 uM of each of the four deoxynucleoside triphosphates (dNTPs), 200 nM of both forward and reverse primer, and ~3-4 ng of environmental DNA template. PCR cycling conditions consisted of an initial denaturation step at 95C for 4 minutes, followed by 35 to 38 cycles of 95C denaturation for 30 sec, 55C annealing for 1 min, 72C extension for 2 min, and a final extension step at 72C for 20 min. For the 2008 borehole fluid sample, a 3-cycle reconditioning PCR was performed in order to help eliminate heteroduplexes (Thompson et al., 2002). Amplification products of the anticipated length were excised from an agarose gel and subsequently purified using the QIAquick gel extraction kit (Qiagen, Valencia, CA). Products were cloned using either the pGEM-T Easy kit (Promega, Madison, WI) or the TOPO TA Cloning kit (Invitrogen, Carlsbad, CA) following the manufacturer’s instructions. Clones were sequenced unidirectionally on an ABI 3730XL DNA Analyzer&nbsp;(Applied Biosystems, Carlsbad, CA).&nbsp;</p>
<p><strong>Fluorescence Microscopy:&nbsp;microbial cell counts<em>&nbsp;</em>&nbsp;</strong>(from&nbsp;<a href="http://www.nature.com/ismej/journal/v7/n1/extref/ismej201273x7.doc">Supplementary Information Document</a>(DOC)&nbsp;for Junbluth et al., 2016).</p>
<p>Sample preparation for microscopy and fluorescence microscopy Fluid samples for microscopy collected in 2011 were prepared in similar fashion to those collected in sampling years 2008-2010 and described previously (Jungbluth et al., 2013). Briefly, 40 to 120 ml sub-samples were fixed with a final concentration of 3% of 0.2 um-filtered formaldehyde for 2 to 4 hours at 4C, and subsequently filtered through 0.2 um pore-sized polycarbonate membranes (Whatman, Maidstone, United Kingdom). After air-drying, membranes were stored desiccated at -80ºC until microscopic analysis. Filter sections were prepared for fluorescence microscopy using a mix of Citifluor/VectaShield/PBS/DAPI as described previously (Jungbluth et al., 2013a). Stained filter sections were inspected with a Leica DM5000B epifluorescence microscope (Leica Microsystems, Wetzlar, Germany) (samples: SSF1-2, SSF4, MIX1-4, SW1-5, SW9-11, SW14-15) or an Eclipse 90i (Nikon Corp., Tokyo, Japan) epifluorescence microscope (all other samples). Both microscopes were equipped with 100x objectives and filter sets appropriate for DAPI fluorescence.</p>
<p><strong>References:</strong></p>
<p>Brewer P, Spencer D (1971). Colorimetric determination of manganese in anoxic waters. Limnol Oceanogr 16: 107-110. doi: 10.4319/lo.1971.16.1.0107</p>
<p>Cowen, James P., et al. "Advanced instrument system for real-time and time-series microbial geochemical sampling of the deep (basaltic) crustal biosphere."&nbsp;<em>Deep Sea Research Part I: Oceanographic Research Papers</em>&nbsp;61 (2012): 43-56. &nbsp;<a href="http://dx.doi.org/10.1016/j.dsr.2011.11.004">http://dx.doi.org/10.1016/j.dsr.2011.11.004</a></p>
<p>Dickson AG, Sabine CL, Christian JR (eds) (2007). Guide to best practices for ocean CO2 measurements, 191pp. (URL: http://cdiac.ornl.gov/oceans/Handbook_2007.html)</p>
<p>Expedition 327 Scientists, 2011. Methods.&nbsp;<em>In</em>&nbsp;Fisher, A.T., Tsuji, T., Petronotis, K., and the Expedition 327 Scientists,&nbsp;<em>Proc. IODP,</em>&nbsp;327: Tokyo (Integrated Ocean Drilling Program Management International, Inc.).</p>
<p>Gibbs C (1976). Characterization and application of ferrozine iron reagent as a ferrous iron indicator. Anal Chem 48: 1197-1201. doi: 10.1021/ac50002a034</p>
<p>Grasshoff K, Kremling K, Ehrhardt M (eds) (1999) Methods of seawater analysis. Wiley: Weinheim. doi: 10.1002/9783527613984</p>
<p>Hedges, J.I., and Stern, J.H., 1984. Carbon and nitrogen determinations of carbonate-containing solids.&nbsp;Limnol. Oceanogr.,&nbsp;29(3):657–663.doi:10.4319/lo.1984.29.3.0657</p>
<p>Jones RD (1991). An improved fluorescence method for the determination of nanomolar concentrations of ammonium in natural-waters. Limnol Oceanogr 36: 814-819. doi: 10.4319/lo.1991.36.4.0814</p>
<p>Jungbluth, Sean P., et al. "Data report: microbial diversity in sediment near Grizzly Bare Seamount in Holes U1363B and U1363G."&nbsp;<em>Proc. IODP&nbsp;Volume</em>. Vol. 327. 2013.&nbsp;<a href="http://dx.doi.org/10.2204/iodp.proc.327.201.2013">http://dx.doi.org/10.2204/iodp.proc.327.201.2013</a></p>
<p>Jungbluth, Sean P., et al. "Novel microbial assemblages inhabiting crustal fluids within mid-ocean ridge flank subsurface basalt."&nbsp;<em>The ISME journal&nbsp;</em>(2016).&nbsp;<a href="http://dx.doi.org/10.1038/ismej.2015.248">dx.doi.org/10.1038/ismej.2015.248</a></p>
<p>Lin, H-T, Hsieh, C-C, Cowen, JP,&nbsp;Rappe, MS (2015). Data report: dissolved and particulate organic carbon in the deep sediments of IODP Site U1363 near Grizzly Bare seamount.&nbsp;<em>Proceedings of the Integrated Ocean Drilling Program&nbsp;</em>327: 1-16. &nbsp;<a href="http://dx.doi.org/10.2204/iodp.proc.327.202.2015">dx.doi.org/10.2204/iodp.proc.327.202.2015</a></p>
<p>Lin, Huei-Ting, et al. "Inorganic chemistry, gas compositions and dissolved organic carbon in fluids from sedimented young basaltic crust on the Juan de Fuca Ridge flanks."&nbsp;<em>Geochimica et Cosmochimica Acta</em>&nbsp;85 (2012): 213-227.&nbsp;<a class="S_C_ddDoi" href="http://dx.doi.org/10.1016/j.gca.2012.02.017" id="ddDoi" target="doilink">http://dx.doi.org/10.1016/j.gca.2012.02.017</a></p>
<p>Phillips BM, Anderson BS, Hunt JW (1997). Measurement and distribution of interstitial and overlying water ammonia and hydrogen sulfide in sediment toxicity tests. Mar Environ Res 44: 117-126. doi: 10.1016/S0141-1136(96)00087-6</p>
<p>Sharp JH, Carlson CA, Peltzer ET, Castle-Ward DM, Savidge KB, Rinker KR (2002a). Final dissolved organic carbon broad community intercalibration and preliminary use of DOC reference materials. Mar Chem 77: 239-253. doi: 10.1016/S0304- 4203(02)00002-6</p>
<p>Sharp JH, Rinker KR, Savidge KB, Abell J, Yves Benaim J, Bronk DA et al. (2002b). A preliminary methods comparison for measurement of dissolved organic nitrogen in seawater. Mar Chem 78: 171-184. doi: 10.1016/S0304-4203(02)00020-8</p>
<p>Stookey LL (1970). Ferrozine- a new spectrophotometric reagent for iron. Anal Chem 42: 779-781. doi: 10.1021/ac60289a016</p>
<p>Thompson JR, Marcelino LA, Polz MF. (2002). Heteroduplexes in mixed-template amplifications: formation, consequence and elimination by 'reconditioning PCR'. <em>Nucleic Acids Res</em> <strong>30:</strong> 2083-2088.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0939564 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0939564
completed
Michael S. Rappé
University of Hawaiʻi at Mānoa
808-372-2394
University of Hawaii at Manoa - Hawaii Institute of Marine Biology 46-007 Lilipuna Rd
Kaneohe
HI
96744
USA
rappe@hawaii.edu
pointOfContact
asNeeded
Unknown
database
Accession_id
Accession_Link
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BioProjectID
description
sample_title
sample_name
organism
collection_date
depth
elev
env_biome
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lon
ph
oxygen
calcium
magnesium
potassium
sodium
chloride
bromide
silicate
ammonium
phosphate
nitrite
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nitrate_and_nitrate
sulfate
dissolved_iron
total_iron
Mn2plus
dissolved_hydrogen_sulfide
dissolved_organic_carbon
TDN
alkalinity
methane
hydrogen
microbial_cell_abundance
ABI 3730XL DNA Analyzer
Dionex ICS-1100s
Thermo Finnigan Delta XP
Orion 911600 Semi-micro pH electrode
pump
TOC-VCSH analyzer
NanoDrop ND-1000 spectrophotometer
theme
None, User defined
brief description
accession number
sample description
date
depth
altitude
site description
site
latitude
longitude
pH
trace element concentration
trace metal concentration
chloride
bromides
silica
Ammonium
reactive phosphorus (PO4)
Nitrite
Nitrate
nitrate plus nitrite
sulfate
sulfide
dissolved organic Carbon
Total Dissolved Nitrogen
total alkalinity (TA)
methane
hydrogen
abundance
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Ion Chromatograph
Mass Spectrometer
pH Sensor
Pump
Shimadzu TOC-V Analyzer
Spectrophotometer
instrument
BCO-DMO Standard Instruments
AT15-35
AT15-55
AT15-66
AT18-07
service
Deployment Activity
Cascadia Basin and JdF Ridge
Guaymas Basin
Pacific North-West
place
Locations
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Center for Dark Energy Biosphere Investigations
http://www.darkenergybiosphere.org
Center for Dark Energy Biosphere Investigations
The mission of the Center for Dark Energy Biosphere Investigations (C-DEBI) is to explore life beneath the seafloor and make transformative discoveries that advance science, benefit society, and inspire people of all ages and origins.
C-DEBI provides a framework for a large, multi-disciplinary group of scientists to pursue fundamental questions about life deep in the sub-surface environment of Earth. The fundamental science questions of C-DEBI involve exploration and discovery, uncovering the processes that constrain the sub-surface biosphere below the oceans, and implications to the Earth system. What type of life exists in this deep biosphere, how much, and how is it distributed and dispersed? What are the physical-chemical conditions that promote or limit life? What are the important oxidation-reduction processes and are they unique or important to humankind? How does this biosphere influence global energy and material cycles, particularly the carbon cycle? Finally, can we discern how such life evolved in geological settings beneath the ocean floor, and how this might relate to ideas about the origin of life on our planet?
C-DEBI's scientific goals are pursued with a combination of approaches:
(1) coordinate, integrate, support, and extend the research associated with four major programs—Juan de Fuca Ridge flank (JdF), South Pacific Gyre (SPG), North Pond (NP), and Dorado Outcrop (DO)—and other field sites;
(2) make substantial investments of resources to support field, laboratory, analytical, and modeling studies of the deep subseafloor ecosystems;
(3) facilitate and encourage synthesis and thematic understanding of submarine microbiological processes, through funding of scientific and technical activities, coordination and hosting of meetings and workshops, and support of (mostly junior) researchers and graduate students; and
(4) entrain, educate, inspire, and mentor an interdisciplinary community of researchers and educators, with an emphasis on undergraduate and graduate students and early-career scientists.
Note: Katrina Edwards was a former PI of C-DEBI; James Cowen is a former co-PI.
Data Management:
C-DEBI is committed to ensuring all the data generated are publically available and deposited in a data repository for long-term storage as stated in their Data Management Plan (PDF) and in compliance with the NSF Ocean Sciences Sample and Data Policy. The data types and products resulting from C-DEBI-supported research include a wide variety of geophysical, geological, geochemical, and biological information, in addition to education and outreach materials, technical documents, and samples. All data and information generated by C-DEBI-supported research projects are required to be made publically available either following publication of research results or within two (2) years of data generation.
To ensure preservation and dissemination of the diverse data-types generated, C-DEBI researchers are working with BCO-DMO Data Managers make data publicly available online. The partnership with BCO-DMO helps ensure that the C-DEBI data are discoverable and available for reuse. Some C-DEBI data is better served by specialized repositories (NCBI's GenBank for sequence data, for example) and, in those cases, BCO-DMO provides dataset documentation (metadata) that includes links to those external repositories.
C-DEBI
largerWorkCitation
program
Microbiology and biogeochemistry of Juan de Fuca Ridge flank borehole fluids
http://www.darkenergybiosphere.org/research/juandefuca.html
Microbiology and biogeochemistry of Juan de Fuca Ridge flank borehole fluids
<p><em>Extracted from the NSF award abstract:</em></p>
<p>Hydrothermally heated fluids circulate everywhere within the permeable basement rock of the upper ocean crust, providing warm temperatures and chemical gradients that support a deep subsurface marine biosphere. The volume of oceanic lithosphere habitable by microbial life is thought to be a substantial portion of the Earth’s crust - extending thousands of meters below the seafloor. During expeditions from 2008 to 2014 we repeatedly sampled basalt-hosted, deep subseafloor crustal fluids from four different boreholes drilled along the Juan de Fuca Ridge flank in the Northeast Pacific Ocean using pumps and samplers capable of collecting whole water and filtered particulates in situ. The instrumented boreholes, sitting at 2600 m depth, penetrate ~100 to 260 m of bottom sediments and another ~48 to 300 m of igneous basement where they tap into hot (up to 65 degrees C), anoxic fluid within Earth’s largest deep subsurface aquifer. Nearby bottom seawater and sediments were sampled as controls. Associated data sets include small subunit ribosomal RNA and functional gene amplicon DNA sequences, metagenome sequences, single cell genome sequences, direct counts of microbial cells and viruses, and a wide range of associated biogeochemical measurements including dissolved gases, particulate and dissolved organic carbon, sulfate, nitrate, and others.</p>
microJdFR
largerWorkCitation
project
eng; USA
oceans
Cascadia Basin and JdF Ridge; Guaymas Basin; Pacific North-West
2016-10-07
Boreholes along the eastern flank of Juan de Fuca Ridge (47N, 128 W)
0
BCO-DMO catalogue of parameters from SSU rRNA gene sequences from marine sediments, marine subseafloor, and deep seawater sampled from the Juan de Fuca Ridge Flank from various R/V Atlantis cruises from 2008-2011 (microJdFR project)
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/661225.rdf
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Units: unitless
Description: <p>Identification number for GenBank; SRA; or IMG databases</p>
http://lod.bco-dmo.org/id/dataset-parameter/661227.rdf
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Units: unitless
Description: <p>URL link to the accession for GenBank; SRA; or IMG</p>
http://lod.bco-dmo.org/id/dataset-parameter/661228.rdf
Name: BioSample_ID
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Description: <p>Identifier for BioSample at NCBI. A BioSample corresponds to descriptions of biological source materials used in experimental assays.</p>
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Units: meters
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Name: elev
Units: meters
Description: <p>Elevation of sample. Sea-water samples are set to sea-level (0) . For sediment and borehole samples, elevation was set equal to the depth of the seafloor (all values negative).</p>
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Description: <p>Biome of sample site</p>
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Description: <p>Environmental features of sample site</p>
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Description: <p>latitutde</p>
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Name: lon
Units: decimal degrees
Description: <p>longitude; west is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/661243.rdf
Name: ph
Units: pH scale
Description: <p>pH</p>
http://lod.bco-dmo.org/id/dataset-parameter/661244.rdf
Name: oxygen
Units: micromoles per liter
Description: <p>oxygen (O2)</p>
http://lod.bco-dmo.org/id/dataset-parameter/661245.rdf
Name: calcium
Units: millimoles per liter
Description: <p>calcium (Ca)</p>
http://lod.bco-dmo.org/id/dataset-parameter/661246.rdf
Name: magnesium
Units: millimoles per liter
Description: <p>magnesium (Mg)</p>
http://lod.bco-dmo.org/id/dataset-parameter/661247.rdf
Name: potassium
Units: millimoles per liter
Description: <p>potassium (K)</p>
http://lod.bco-dmo.org/id/dataset-parameter/661248.rdf
Name: sodium
Units: millimoles per liter
Description: <p>sodium (Na)</p>
http://lod.bco-dmo.org/id/dataset-parameter/661249.rdf
Name: chloride
Units: millimoles per liter
Description: <p>chloride (Cl-)</p>
http://lod.bco-dmo.org/id/dataset-parameter/661250.rdf
Name: bromide
Units: millimoles per liter
Description: <p>bromide (Br-)</p>
http://lod.bco-dmo.org/id/dataset-parameter/661251.rdf
Name: silicate
Units: micromoles per liter
Description: <p>silicon dioxide (SiO2)</p>
http://lod.bco-dmo.org/id/dataset-parameter/661252.rdf
Name: ammonium
Units: micromoles per liter
Description: <p>ammonium (NH4)</p>
http://lod.bco-dmo.org/id/dataset-parameter/661253.rdf
Name: phosphate
Units: micromoles per liter
Description: <p>phosphate (PO4)</p>
http://lod.bco-dmo.org/id/dataset-parameter/661254.rdf
Name: nitrite
Units: micromoles per liter
Description: <p>nitrite (NO2)</p>
http://lod.bco-dmo.org/id/dataset-parameter/661255.rdf
Name: nitrate
Units: micromoles per liter
Description: <p>nitrate (NO3)</p>
http://lod.bco-dmo.org/id/dataset-parameter/661256.rdf
Name: nitrate_and_nitrate
Units: micromoles per liter
Description: <p>combined nitrate and nitrate (NO3 and NO2)</p>
http://lod.bco-dmo.org/id/dataset-parameter/661257.rdf
Name: sulfate
Units: millimoles per liter
Description: <p>sulfate (SO4)</p>
http://lod.bco-dmo.org/id/dataset-parameter/661258.rdf
Name: dissolved_iron
Units: micromoles per liter
Description: <p>dissolved iron (dFe)</p>
http://lod.bco-dmo.org/id/dataset-parameter/661259.rdf
Name: total_iron
Units: micromoles per liter
Description: <p>total iron (Fe)</p>
http://lod.bco-dmo.org/id/dataset-parameter/661260.rdf
Name: Mn2plus
Units: micromoles per liter
Description: <p>Manganese ion (Mn2+)</p>
http://lod.bco-dmo.org/id/dataset-parameter/661261.rdf
Name: dissolved_hydrogen_sulfide
Units: micromoles per liter
Description: <p>dissolved hydrogen sulfide (dissolved H2S)</p>
http://lod.bco-dmo.org/id/dataset-parameter/661262.rdf
Name: dissolved_organic_carbon
Units: micromoles per liter
Description: <p>dissolved organic carbon (DOC)</p>
http://lod.bco-dmo.org/id/dataset-parameter/661263.rdf
Name: TDN
Units: micromoles per liter
Description: <p>total dissolved nitrogen (TDN)</p>
http://lod.bco-dmo.org/id/dataset-parameter/661264.rdf
Name: alkalinity
Units: milliequivalents per liter
Description: <p>alkalinity</p>
http://lod.bco-dmo.org/id/dataset-parameter/661265.rdf
Name: methane
Units: micromoles per liter
Description: <p>methane (CH4)</p>
http://lod.bco-dmo.org/id/dataset-parameter/661266.rdf
Name: hydrogen
Units: micromoles per liter
Description: <p>hydrogen (H)</p>
http://lod.bco-dmo.org/id/dataset-parameter/661267.rdf
Name: microbial_cell_abundance
Units: cells per milliliter
Description: <p>microbial cell abundance</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
412731
https://datadocs.bco-dmo.org/file/WWW1rOXijQlKLp/accessions.csv
accessions.csv
Primary data file for dataset ID 660489
download
https://osprey.bco-dmo.org/dataset/660489/data/download
download
onLine
dataset
<p><strong>Sampling Methodology:</strong></p>
<p>Sediment coring was performed by the IODP (described in Expedition 327 Scientists, 2011; <em>Integrated Ocean Drilling Program</em>). SSU rRNA genes were obtained as described in Jungbluth et al., 2013; <em>Proceedings of the Integrated Ocean Drilling Program</em> (see <a href="http://www.nature.com/ismej/journal/v7/n1/extref/ismej201273x7.doc">Supplementary Information Document</a>(.DOC)&nbsp;for this publication).</p>
<p>CORK borehole fluids were sampled using a custom-built water sampler (described in Cowen et al., 2012). For a detailed description of the pump system&nbsp;see&nbsp;<a href="http://dx.doi.org/10.1016/j.gca.2012.02.017">Lin, et al. 2012</a>.</p>
<p><strong>Pore water&nbsp;dissolved organic carbon (</strong>from&nbsp;Lin et al., 2015<em>&nbsp;</em><a href="http://publications.iodp.org/proceedings/327/202/202_3.htm">Materials and Methods&nbsp;</a>).</p>
<p>Sedimentary pore water DOC concentrations were measured by high-temperature combustion using a Shimadzu TOC-VCSH analyzer. The combustion temperature was set at 720C to ensure complete oxidation of organic matter. Samples were acidified to pH &lt;2 by the addition of 45 uL of 2 M HCl to 3 mL samples. No acid contamination was observed based on monitoring the DOC value of low-carbon deionized water. Samples were purged with nitrogen gas within the autosampler syringe for 2 min in order to remove inorganic carbon. An injection volume of 150 uL was used, with five or six injections per sample. The reproducibility between replicate injections was &lt;1 uM. Analytical reference materials (ARM) supplied by Dr. Dennis Hansell (RSMAS, University of Miami) were measured before, between, and after analysis of environmental samples (Sharp et al., 2002; Dickson et al., 2007). At least one ARM was measured every five samples. The average measured concentration of the ARM was 42 plus or minus 2 uM (n&nbsp;= 44); the reported value was 41–43 uM. Our detection limit for DOC concentrations was ~2 uM.</p>
<p><strong>Sediment organic carbon and nitrogen &nbsp;(</strong>relevant text extracted from&nbsp;Lin et al., 2015<em>&nbsp;</em><a href="http://publications.iodp.org/proceedings/327/202/202_3.htm">Materials and Methods&nbsp;</a>).</p>
<p>Whole sediment samples were analyzed for concentration of total carbon, organic carbon, and total nitrogen using an elemental combustion system (Costech ECS 4010) connected inline to an isotope-ratio mass spectrometer (Thermo Finnigan Delta XP). The amount of powdered sediment used for the analyses was optimized to provide sufficient carbon and nitrogen for isotopic composition analysis and varied between 26 and 425 mg. A subset of samples was acidified by fuming with concentrated HCl (Hedges and Stern, 1984) in order to remove inorganic carbon and quantify the particulate organic carbon (POC) content. Acid fuming did not remove inorganic nitrogen, resulting in insignificant differences between whole and acid-fumed total particulate nitrogen (PN) concentrations.</p>
<p><strong>Analytical methods for&nbsp;geochemistry </strong></p>
<p>Text below extracted from <a href="http://www.nature.com/ismej/journal/v10/n8/extref/ismej2015248x1.pdf">Supplementary Information</a> (PDF)&nbsp;Junbluth et al., 2016. &nbsp;See reference for full description.</p>
<p>Major ions (Ca2+, Mg2+, K+ , Na+, Cl- , SO4 2- and Br- ) were analyzed by ion chromatography on a Dionex ICS-1100s (Sunnyvale, CA, USA). In addition, magnesium and calcium concentrations were also analyzed by EDTA (colorimetric) and EGTA (electrometric) titration (Grasshoff et al., 1999), or inductively coupled plasma optical emission spectroscopy (ICP-OES) (Lin et al., 2012).&nbsp;</p>
<p>Silicate, nitrate, nitrite, phosphate, dissolved sulfide and dissolved manganese concentrations were measured by colorimetry (Brewer and Spencer, 1971; Phillips et al., 1997; Grasshoff et al., 1999).&nbsp;</p>
<p>&nbsp;Ammonium concentrations were measured by a flow injection-fluorometric method (Jones, 1991). The detection limit was ~2 µM for ammonium in basement fluids and the analytical uncertainty is 0.5 µM.</p>
<p>Ferrous iron was measured directly by a Ferrozine colorimetry method (Stookey, 1970; Gibbs, 1976).</p>
<p>For total iron analysis, samples were first reduced with ascorbic acid and analyzed as ferrous iron. The detection limit for both ferrous iron and total iron was 0.1 µM.</p>
<p>Dissolved organic carbon (DOC) was measured by high-temperature combustion using a TOC-VCSH analyzer (Sharp et al., 2002a; Dickson et al., 2007) (Shimadzu Corp., Kyoto, Japan).&nbsp;</p>
<p>Total dissolved nitrogen (TDN) was measured with a chemiluminescence detector in-line with a Shimadzu TOC-VCSH analyzer (Sharp et al., 2002b).</p>
<p>Alkalinity was determined by acid titration. Acid (0.1N HCl) was standardized with CO2 certified reference materials (CRMs) purchased from the office of Andrew Dickson at Scripps Institution of Oceanography.&nbsp;</p>
<p>An Orion 911600 Semi-micro pH electrode (ThermoFisher Scientific, Waltham, MA, USA) was used to measure the pH and electrode potential during the titration process. The Gran function plot method was used to evaluate titration end-points and calculate sample alkalinity (Dickson et al., 2007). The analytical reproducibility for alkalinity measurements was &lt;0.02 mM.</p>
<p><strong>SSU rRNA gene cloning and sequencing&nbsp;</strong>(from&nbsp;<a href="http://www.nature.com/ismej/journal/v7/n1/extref/ismej201273x7.doc">Supplementary Information Document</a>(DOC)&nbsp;for Junbluth et al., 2013).</p>
<p>Small subunit ribosomal RNA (SSU rRNA) gene fragments were amplified via the polymerase chain reaction (PCR) using the universal oligonucleotide forward and reverse primers 519F (5’-CAGCMGCCGCGGTAATWC-3’) and 1406R (5’-ACGGGCGGTGTGTRC-3’), respectively. Each 20 ul PCR reaction contained 0.25 U of PicoMaxx high fidelity DNA polymerase (Stratagene, La Jolla, CA), 1x PicoMaxx reaction buffer, 200 uM of each of the four deoxynucleoside triphosphates (dNTPs), 200 nM of both forward and reverse primer, and ~3-4 ng of environmental DNA template. PCR cycling conditions consisted of an initial denaturation step at 95C for 4 minutes, followed by 35 to 38 cycles of 95C denaturation for 30 sec, 55C annealing for 1 min, 72C extension for 2 min, and a final extension step at 72C for 20 min. For the 2008 borehole fluid sample, a 3-cycle reconditioning PCR was performed in order to help eliminate heteroduplexes (Thompson et al., 2002). Amplification products of the anticipated length were excised from an agarose gel and subsequently purified using the QIAquick gel extraction kit (Qiagen, Valencia, CA). Products were cloned using either the pGEM-T Easy kit (Promega, Madison, WI) or the TOPO TA Cloning kit (Invitrogen, Carlsbad, CA) following the manufacturer’s instructions. Clones were sequenced unidirectionally on an ABI 3730XL DNA Analyzer&nbsp;(Applied Biosystems, Carlsbad, CA).&nbsp;</p>
<p><strong>Fluorescence Microscopy:&nbsp;microbial cell counts<em>&nbsp;</em>&nbsp;</strong>(from&nbsp;<a href="http://www.nature.com/ismej/journal/v7/n1/extref/ismej201273x7.doc">Supplementary Information Document</a>(DOC)&nbsp;for Junbluth et al., 2016).</p>
<p>Sample preparation for microscopy and fluorescence microscopy Fluid samples for microscopy collected in 2011 were prepared in similar fashion to those collected in sampling years 2008-2010 and described previously (Jungbluth et al., 2013). Briefly, 40 to 120 ml sub-samples were fixed with a final concentration of 3% of 0.2 um-filtered formaldehyde for 2 to 4 hours at 4C, and subsequently filtered through 0.2 um pore-sized polycarbonate membranes (Whatman, Maidstone, United Kingdom). After air-drying, membranes were stored desiccated at -80ºC until microscopic analysis. Filter sections were prepared for fluorescence microscopy using a mix of Citifluor/VectaShield/PBS/DAPI as described previously (Jungbluth et al., 2013a). Stained filter sections were inspected with a Leica DM5000B epifluorescence microscope (Leica Microsystems, Wetzlar, Germany) (samples: SSF1-2, SSF4, MIX1-4, SW1-5, SW9-11, SW14-15) or an Eclipse 90i (Nikon Corp., Tokyo, Japan) epifluorescence microscope (all other samples). Both microscopes were equipped with 100x objectives and filter sets appropriate for DAPI fluorescence.</p>
<p><strong>References:</strong></p>
<p>Brewer P, Spencer D (1971). Colorimetric determination of manganese in anoxic waters. Limnol Oceanogr 16: 107-110. doi: 10.4319/lo.1971.16.1.0107</p>
<p>Cowen, James P., et al. "Advanced instrument system for real-time and time-series microbial geochemical sampling of the deep (basaltic) crustal biosphere."&nbsp;<em>Deep Sea Research Part I: Oceanographic Research Papers</em>&nbsp;61 (2012): 43-56. &nbsp;<a href="http://dx.doi.org/10.1016/j.dsr.2011.11.004">http://dx.doi.org/10.1016/j.dsr.2011.11.004</a></p>
<p>Dickson AG, Sabine CL, Christian JR (eds) (2007). Guide to best practices for ocean CO2 measurements, 191pp. (URL: http://cdiac.ornl.gov/oceans/Handbook_2007.html)</p>
<p>Expedition 327 Scientists, 2011. Methods.&nbsp;<em>In</em>&nbsp;Fisher, A.T., Tsuji, T., Petronotis, K., and the Expedition 327 Scientists,&nbsp;<em>Proc. IODP,</em>&nbsp;327: Tokyo (Integrated Ocean Drilling Program Management International, Inc.).</p>
<p>Gibbs C (1976). Characterization and application of ferrozine iron reagent as a ferrous iron indicator. Anal Chem 48: 1197-1201. doi: 10.1021/ac50002a034</p>
<p>Grasshoff K, Kremling K, Ehrhardt M (eds) (1999) Methods of seawater analysis. Wiley: Weinheim. doi: 10.1002/9783527613984</p>
<p>Hedges, J.I., and Stern, J.H., 1984. Carbon and nitrogen determinations of carbonate-containing solids.&nbsp;Limnol. Oceanogr.,&nbsp;29(3):657–663.doi:10.4319/lo.1984.29.3.0657</p>
<p>Jones RD (1991). An improved fluorescence method for the determination of nanomolar concentrations of ammonium in natural-waters. Limnol Oceanogr 36: 814-819. doi: 10.4319/lo.1991.36.4.0814</p>
<p>Jungbluth, Sean P., et al. "Data report: microbial diversity in sediment near Grizzly Bare Seamount in Holes U1363B and U1363G."&nbsp;<em>Proc. IODP&nbsp;Volume</em>. Vol. 327. 2013.&nbsp;<a href="http://dx.doi.org/10.2204/iodp.proc.327.201.2013">http://dx.doi.org/10.2204/iodp.proc.327.201.2013</a></p>
<p>Jungbluth, Sean P., et al. "Novel microbial assemblages inhabiting crustal fluids within mid-ocean ridge flank subsurface basalt."&nbsp;<em>The ISME journal&nbsp;</em>(2016).&nbsp;<a href="http://dx.doi.org/10.1038/ismej.2015.248">dx.doi.org/10.1038/ismej.2015.248</a></p>
<p>Lin, H-T, Hsieh, C-C, Cowen, JP,&nbsp;Rappe, MS (2015). Data report: dissolved and particulate organic carbon in the deep sediments of IODP Site U1363 near Grizzly Bare seamount.&nbsp;<em>Proceedings of the Integrated Ocean Drilling Program&nbsp;</em>327: 1-16. &nbsp;<a href="http://dx.doi.org/10.2204/iodp.proc.327.202.2015">dx.doi.org/10.2204/iodp.proc.327.202.2015</a></p>
<p>Lin, Huei-Ting, et al. "Inorganic chemistry, gas compositions and dissolved organic carbon in fluids from sedimented young basaltic crust on the Juan de Fuca Ridge flanks."&nbsp;<em>Geochimica et Cosmochimica Acta</em>&nbsp;85 (2012): 213-227.&nbsp;<a class="S_C_ddDoi" href="http://dx.doi.org/10.1016/j.gca.2012.02.017" id="ddDoi" target="doilink">http://dx.doi.org/10.1016/j.gca.2012.02.017</a></p>
<p>Phillips BM, Anderson BS, Hunt JW (1997). Measurement and distribution of interstitial and overlying water ammonia and hydrogen sulfide in sediment toxicity tests. Mar Environ Res 44: 117-126. doi: 10.1016/S0141-1136(96)00087-6</p>
<p>Sharp JH, Carlson CA, Peltzer ET, Castle-Ward DM, Savidge KB, Rinker KR (2002a). Final dissolved organic carbon broad community intercalibration and preliminary use of DOC reference materials. Mar Chem 77: 239-253. doi: 10.1016/S0304- 4203(02)00002-6</p>
<p>Sharp JH, Rinker KR, Savidge KB, Abell J, Yves Benaim J, Bronk DA et al. (2002b). A preliminary methods comparison for measurement of dissolved organic nitrogen in seawater. Mar Chem 78: 171-184. doi: 10.1016/S0304-4203(02)00020-8</p>
<p>Stookey LL (1970). Ferrozine- a new spectrophotometric reagent for iron. Anal Chem 42: 779-781. doi: 10.1021/ac60289a016</p>
<p>Thompson JR, Marcelino LA, Polz MF. (2002). Heteroduplexes in mixed-template amplifications: formation, consequence and elimination by 'reconditioning PCR'. <em>Nucleic Acids Res</em> <strong>30:</strong> 2083-2088.</p>
from Cruise: AT15-35 <p>R/V Atlantis – AT15-35 – HOV Alvin II dive 4432</p>
from Cruise: AT15-55 <p>R/V Atlantis - AT15-51 - HOV Alvin II dives 4532, 4533, 4434, 4536, & 4537</p>
from Cruise: AT15-66 <p>R/V Atlantis - AT15-66 - ROV Jason II dives J2-497, J2-498, J2-499, J2-502, J2-503, & J2-505, J2-500</p>
from Cruise: AT18-07 <p>R/V Atlantis - AT18-07 - ROV Jason II dives J2-566, J2-569, J2-571, & J2-573</p>
Specified by the Principal Investigator(s)
<p>These data have been quality controlled as described in Jungbluth et al., 2013, and&nbsp;Jungbluth et al., 2016.</p>
<p>For seawater samples, elevation was set equal to sea-level (value: 0) and all sample depths are reported as positive values.<br />
For sediment and borehole samples, elevation was set equal to the depth of the seafloor (all values negative) and depths into the seafloor are reported as positive values.</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
ABI 3730XL DNA Analyzer
ABI 3730XL DNA Analyzer
PI Supplied Instrument Name: ABI 3730XL DNA Analyzer PI Supplied Instrument Description:Clones were sequenced unidirectionally on an ABI 3730XL DNA Analyzer (Applied Biosystems, Carlsbad, CA). Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
Dionex ICS-1100s
Dionex ICS-1100s
PI Supplied Instrument Name: Dionex ICS-1100s Instrument Name: Ion Chromatograph Instrument Short Name:Ion Chromatograph Instrument Description: Ion chromatography is a form of liquid chromatography that measures concentrations of ionic species by separating them based on their interaction with a resin. Ionic species separate differently depending on species type and size. Ion chromatographs are able to measure concentrations of major anions, such as fluoride, chloride, nitrate, nitrite, and sulfate, as well as major cations such as lithium, sodium, ammonium, potassium, calcium, and magnesium in the parts-per-billion (ppb) range. (from http://serc.carleton.edu/microbelife/research_methods/biogeochemical/ic.html)
Thermo Finnigan Delta XP
Thermo Finnigan Delta XP
PI Supplied Instrument Name: Thermo Finnigan Delta XP PI Supplied Instrument Description:Whole sediment samples were analyzed for concentration and isotopic composition of total carbon, organic carbon, and total nitrogen using an elemental combustion system (Costech ECS 4010) connected inline to an isotope-ratio mass spectrometer (Thermo Finnigan Delta XP). Instrument Name: Mass Spectrometer Instrument Short Name:Mass Spec Instrument Description: General term for instruments used to measure the mass-to-charge ratio of ions; generally used to find the composition of a sample by generating a mass spectrum representing the masses of sample components. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/
Orion 911600 Semi-micro pH electrode
Orion 911600 Semi-micro pH electrode
PI Supplied Instrument Name: Orion 911600 Semi-micro pH electrode PI Supplied Instrument Description: Orion 911600 Semi-micro pH electrode (ThermoFisher Scientific, Waltham, MA, USA) Instrument Name: pH Sensor Instrument Short Name:pH Sensor Instrument Description: An instrument that measures the hydrogen ion activity in solutions.
The overall concentration of hydrogen ions is inversely related to its pH. The pH scale ranges from 0 to 14 and indicates whether acidic (more H+) or basic (less H+).
pump
pump
PI Supplied Instrument Name: pump PI Supplied Instrument Description:A custom pump system was used to sample basement fluid. It connected to the CORK observatorys' fluid delivery lines. The design of this system changed over the course of the study. It included the pump components Pelagic Electronics 5010 series deep sea pump, and Sea-Bird SBE-5T submersible titanium pump. For a detailed description see:
Lin, Huei-Ting, et al. "Inorganic chemistry, gas compositions and dissolved organic carbon in fluids from sedimented young basaltic crust on the Juan de Fuca Ridge flanks." Geochimica et Cosmochimica Acta 85 (2012): 213-227. http://dx.doi.org/10.1016/j.gca.2012.02.017 Instrument Name: Pump Instrument Short Name: Instrument Description: A pump is a device that moves fluids (liquids or gases), or sometimes slurries, by mechanical action. Pumps can be classified into three major groups according to the method they use to move the fluid: direct lift, displacement, and gravity pumps
TOC-VCSH analyzer
TOC-VCSH analyzer
PI Supplied Instrument Name: TOC-VCSH analyzer Instrument Name: Shimadzu TOC-V Analyzer Instrument Short Name:Shimadzu TOC-V Instrument Description: A Shimadzu TOC-V Analyzer measures DOC by high temperature combustion method. Community Standard Description: http://onto.nerc.ac.uk/CAST/124
NanoDrop ND-1000 spectrophotometer
NanoDrop ND-1000 spectrophotometer
PI Supplied Instrument Name: NanoDrop ND-1000 spectrophotometer PI Supplied Instrument Description:NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA) was used to quantify resulting genomic DNA. Instrument Name: Spectrophotometer Instrument Short Name:Spectrophotometer Instrument Description: An instrument used to measure the relative absorption of electromagnetic radiation of different wavelengths in the near infra-red, visible and ultraviolet wavebands by samples. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB20/
Cruise: AT15-35
AT15-35
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
AT15-35
James Cowen
University of Hawaiʻi at Mānoa
Cruise: AT15-55
AT15-55
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
AT15-55
Anna-Louise Reysenbach
Portland State University
Cruise: AT15-66
AT15-66
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
AT15-66
James Cowen
University of Hawai'i
Cruise: AT18-07
AT18-07
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
AT18-07
Andrew Fisher
University of California-Santa Cruz
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel