http://lod.bco-dmo.org/id/dataset/543286
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
2014-12-19
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Physical and chemical metadata for microbiological samples from R/V New Horizon cruises GoCAL1, GoCAL2, GoCAL3 in the Guaymas Basin, Gulf of California from 2004-2005 (Guaymas plumes project)
2014-12-19
publication
2014-12-19
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-12-28
publication
https://doi.org/10.26008/1912/bco-dmo.543286.1
Gregory J. Dick
University of Michigan
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: Dick, G. J. (2021) Physical and chemical metadata for microbiological samples from R/V New Horizon cruises GoCAL1, GoCAL2, GoCAL3 in the Guaymas Basin, Gulf of California from 2004-2005 (Guaymas plumes project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2014-12-19 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.543286.1 [access date]
Physical and chemical metadata for microbiological samples from Guaymas Basin plumes. Dataset Description: <p>Physical and chemical metadata (sal, Mn, O2, temp, etc.) for microbiological samples from Guyamas Basin plumes.</p>
<p><em>The following publications are associated with this data:</em><br />
Anantharaman, K.A., M.B. Duhaime, J.A. Breier, K. Wendt, B.M. Toner, and G.J. Dick (2014). Sulfur oxidation genes in diverse deep-sea viruses. Science 344: 757-760. doi:<a href="http://dx.doi.org/10.1126/science.1252229" target="_blank">10.1126/science.1252229 </a></p>
<p>Li, M., B.M. Toner, B.J. Baker, J.A. Breier, C.S. Sheik, and G.J. Dick (2014). Microbial iron uptake as a mechanism for dispersing iron from deep-sea hydrothermal vents. Nature Communications 5: 3192. doi:<a href="http://dx.doi.org/10.1038/ncomms4192" target="_blank">10.1038/ncomms4192</a></p>
<p>Li, M., S. Jain, B.J. Baker, C. Taylor, and G.J. Dick (2014). Novel hydrocarbon monooxygenase genes in the metatranscriptome of a natural deep-sea hydrocarbon plume. Environmental Microbiology 16: 60-71. doi:<a href="http://dx.doi.org/10.1111/1462-2920.12182" target="_blank">10.1111/1462-2920.12182</a></p>
<p>Sheik, C.S. 2, S. Jain, and G.J. Dick (2014). Metabolic flexibility of enigmatic SAR324 revealed through metagenomics and metatranscriptomics. Environmental Microbiology 16: 304-317. doi:<a href="http://dx.doi.org/10.1111/1462-2920.12165" target="_blank">10.1111/1462-2920.12165</a></p>
<p>Baker, B.J., C.S. Sheik, C.A. Taylor, S. Jain, A. Bhasi, J.D. Cavalcoli, and G.J. Dick (2013). Community transcriptomic assembly reveals microbes that contribute to deep-sea carbon and nitrogen cycling. The ISME Journal 7: 1962-1973. doi:<a href="http://dx.doi.org/10.1038/ismej.2013.85" target="_blank">10.1038/ismej.2013.85</a></p>
<p>Dick, G.J., K. Anantharaman, B.J. Baker, M. Li, D.C. Reed, and C.S. Sheik (2013). Hydrothermal vent plume microbiology: ecological and biogeographic linkages to seafloor and water column habitats. Frontiers in Microbiology 4: 124. doi:<a href="http://dx.doi.org/10.3389/fmicb.2013.00124" target="_blank">10.3389/fmicb.2013.00124 </a></p>
<p>Anantharaman, K., J.A. Breier, C.S. Sheik, and G.J. Dick (2013). Evidence for hydrogen oxidation and metabolic plasticity in widespread deep-sea bacteria. Proceedings of the National Academy of Sciences 110: 330-335. doi:<a href="http://dx.doi.org/10.1073/pnas.1215340110" target="_blank">10.1073/pnas.1215340110</a></p>
<p>Baker, B.J., R.A. Lesniewski, and G.J. Dick. Genome-enabled transcriptomics reveals archaeal populations that drive nitrification in a deep-sea hydrothermal plume (2012). The ISME Journal 6: 2269-2279. doi:<a href="http://dx.doi.org/10.1038/ismej.2012.64" target="_blank">10.1038/ismej.2012.64</a></p>
<p>Lesniewski, R.A., S. Jain, P.D. Schloss, K. Anantharaman,and G.J. Dick (2012). The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and chemolithotrophs. The ISME Journal 6: 2257-2268. doi:<a href="http://dx.doi.org/10.1038/ismej.2012.63" target="_blank">10.1038/ismej.2012.63</a></p> Methods and Sampling: <p>Hydrothermal plumes were detected by turbidity anomalies as measured by an air-calibrated transmissometer (WetLabs) on a CTD rosette (Sea-Bird). Water samples were collected in 10-L niskin bottles by CTD Rosette (Sea-Bird).</p>
<p>Samples were transferred from niskin bottles to acidwashed 50 mL polypropylene tubes. Samples for dissolved Mn (dMn) were filtered through 0.2 um acid-washed nucleopore polycarbonate filters within 1 h of collection. Filtrate (dMn) and unfiltered total Mn samples (tMn) were stabilized by acidification acidification with Optima grade nitric acid to a pH of &lt;2 and stored at 4 degrees C until analysis. All shipboard manipulations were performed in a laminar flow hood with clean techniques. Mn concentrations were determined on a Thermoquest Finnigan Element 2 double focusing, single collector, magnetic sector inductively coupled plasma mass spectrometer (ICP-MS) at the SIO unified laboratory analytical facility. ICP-MS was done at low resolution following instrument and induction parameters described previously (Field et al., 1999). Samples were diluted 1:50 in 2% nitric acid in quartz-distilled (QD) water prior to analysis. A calibration curve was prepared as described previously (Rodushkin and Ruth, 1998) using matrix-matched external standards made with 2% natural seawater stripped of metals by precipitation with Optima ammonium hydroxide. Indium (1 ppb) was used as an internal standard in all standards and samples. Standard additions (Willard et al., 1965) were used to rule out a matrix effect. To confirm analytical accuracy, reference waters CASS-4 and NASS-5 (Verplank et al., 2001) were included in the analysis as samples. Our experimentally determined average Mn concentration for CASS was 56 ± 10 nM (reported to be 51 nM) and for NASS-5 it was16 ± 8 nM (reported to be 17 nM). Six samples from station 1 were collected, processed and analyzed in duplicate. The average standard deviation was 8 nM, which includes variation due to both sampling and analytical error.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1029242 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1029242
Funding provided by Gordon and Betty Moore Foundation (GBMF) Award Number: GBMF2609 Award URL: http://www.moore.org/grants/list/GBMF2609
completed
Gregory J. Dick
University of Michigan
734-763-3228
Department of Earth and Environmental Sciences 1100 N. University Ave., 2534 CC Little Building
Ann Arbor
MI
48109-1005
USA
gdick@umich.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
sample
sample_type
month
day
year
date
cast
lat
lon
depth_w
depth
sal
Mn_tot
Mn_diss
O2
temp
filter_type
filter_pore_size
CTD Sea-Bird
Thermoquest Finnigan Element 2
Niskin bottle
Transmissometer
theme
None, User defined
sample identification
sample type
month of year
day of month
year
date
cast
latitude
longitude
depth_w
depth
salinity
Manganese
dissolved Oxygen
water temperature at measurement depth
No BCO-DMO term
filter_size
featureType
BCO-DMO Standard Parameters
CTD Sea-Bird
Inductively Coupled Plasma Mass Spectrometer
Niskin bottle
Transmissometer
instrument
BCO-DMO Standard Instruments
GoCAL1
GoCAL2
GoCAL3
service
Deployment Activity
Guaymas Basin, Gulf of California
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.
Linking biogeochemistry and microbial community dynamics in deep-sea hydrothermal plumes
http://www.earth.lsa.umich.edu/geomicrobiology/Guaymas.html
Linking biogeochemistry and microbial community dynamics in deep-sea hydrothermal plumes
<p><em>Description from NSF award abstract:</em><br />
Deep-sea hydrothermal vent plumes are globally distributed along the 60,000-km mid-ocean ridge system and are hot spots of microbial biogeochemistry in the deep oceans. These plumes play host to important interactions between microbial communities and hydrothermal inputs; hydrothermal energy sources stimulate enhanced microbial activity and productivity, and microorganisms mediate the flux of elements and energy from deep-sea hydrothermal vents into the oceans. This hydrothermal flux is a significant source of two key micronutrients, iron and manganese, for the oceans. Despite this importance, microbial communities in deep sea-hydrothermal plumes have been understudied relative to those inhabiting near-vent and subsurface environments. The overall goal of this project is to reveal the microbial community dynamics responsible for enhanced microbial activities and mediation of geochemical processes that has been observed in deep-sea hydrothermal plumes. This research project is focused on plumes in the Guaymas Basin (Gulf of California), where previous results showed dramatic enhancement of microbial activity and enzymatic manganese (II) oxidation relative to the ambient deep sea. Cutting-edge DNA sequencing technologies will be utilized to characterize the microbial diversity, metabolic potential and physiological state of plume versus background communities through metagenomics and metatranscriptomics. The specific objectives are:<br />
(1) to utilize hundreds of thousands of rRNA gene sequences available from DNA and RNA to compare community structure and population-specific activity in plumes versus background;<br />
(2) to reconstruct composite genomes from the most abundant deep-sea microbial populations and evaluate their metabolic capabilities and nutritional needs; and<br />
(3) to quantitatively compare gene content and expression profiles in plume and background, with a focus on uncovering metabolic shifts towards chemolithoautotrophy.</p>
<p>Overall, results are expected to shed light on the nature of microbial players and processes in plumes: is plume biogeochemistry mediated by indigenous deep-sea microorganisms that have been stimulated by hydrothermal inputs, or by plume-specific groups that were entrained from near-vent environments?</p>
Guaymas plumes
largerWorkCitation
project
eng; USA
oceans
Guaymas Basin, Gulf of California
-111.4109
-110.72388
26.37925
27.506
2004-07-11
2005-02-05
Guaymas Basin and Carmen Basin, Gulf of California
0
BCO-DMO catalogue of parameters from Physical and chemical metadata for microbiological samples from R/V New Horizon cruises GoCAL1, GoCAL2, GoCAL3 in the Guaymas Basin, Gulf of California from 2004-2005 (Guaymas plumes 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/543296.rdf
Name: sample
Units: unitless
Description: <p>Sample identification number.</p>
http://lod.bco-dmo.org/id/dataset-parameter/543297.rdf
Name: sample_type
Units: text
Description: <p>Type of sample.</p>
http://lod.bco-dmo.org/id/dataset-parameter/543298.rdf
Name: month
Units: mm (01-12)
Description: <p>2-digit month.</p>
http://lod.bco-dmo.org/id/dataset-parameter/543299.rdf
Name: day
Units: dd (01-31)
Description: <p>2-digit day of month.</p>
http://lod.bco-dmo.org/id/dataset-parameter/543300.rdf
Name: year
Units: YYYY
Description: <p>4-digit year</p>
http://lod.bco-dmo.org/id/dataset-parameter/543301.rdf
Name: date
Units: mm/dd/yyyy
Description: <p>Date formatted as month/day/year.</p>
http://lod.bco-dmo.org/id/dataset-parameter/543302.rdf
Name: cast
Units: unitless
Description: <p>Cast identification number.</p>
http://lod.bco-dmo.org/id/dataset-parameter/543303.rdf
Name: lat
Units: decimal degrees
Description: <p>Latitude. Positive values = North.</p>
http://lod.bco-dmo.org/id/dataset-parameter/543304.rdf
Name: lon
Units: decimal degrees
Description: <p>Longitude. Negative values = West.</p>
http://lod.bco-dmo.org/id/dataset-parameter/543305.rdf
Name: depth_w
Units: meters (m)
Description: <p>Depth of the water.</p>
http://lod.bco-dmo.org/id/dataset-parameter/543306.rdf
Name: depth
Units: meters (m)
Description: <p>Sample depth.</p>
http://lod.bco-dmo.org/id/dataset-parameter/543307.rdf
Name: sal
Units: parts per million (ppm)
Description: <p>Salinity.</p>
http://lod.bco-dmo.org/id/dataset-parameter/543308.rdf
Name: Mn_tot
Units: nanomolar (nM)
Description: <p>Total Manganese (Mn) concentration.</p>
http://lod.bco-dmo.org/id/dataset-parameter/543309.rdf
Name: Mn_diss
Units: nanomolar (nM)
Description: <p>Dissolved Manganese (Mn) concentration.</p>
http://lod.bco-dmo.org/id/dataset-parameter/543310.rdf
Name: O2
Units: micromolar (um)
Description: <p>Oxygen (O2) concentration.</p>
http://lod.bco-dmo.org/id/dataset-parameter/543311.rdf
Name: temp
Units: degrees Celsius (C )
Description: <p>Temperature.</p>
http://lod.bco-dmo.org/id/dataset-parameter/543312.rdf
Name: filter_type
Units: text
Description: <p>Type of filter.</p>
http://lod.bco-dmo.org/id/dataset-parameter/543313.rdf
Name: filter_pore_size
Units: micrometers (um)
Description: <p>Pore size of the filter.</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
834
https://darchive.mblwhoilibrary.org/bitstream/1912/27873/1/dataset-543286_physical-and-chemical-data__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.543286.1
download
onLine
dataset
<p>Hydrothermal plumes were detected by turbidity anomalies as measured by an air-calibrated transmissometer (WetLabs) on a CTD rosette (Sea-Bird). Water samples were collected in 10-L niskin bottles by CTD Rosette (Sea-Bird).</p>
<p>Samples were transferred from niskin bottles to acidwashed 50 mL polypropylene tubes. Samples for dissolved Mn (dMn) were filtered through 0.2 um acid-washed nucleopore polycarbonate filters within 1 h of collection. Filtrate (dMn) and unfiltered total Mn samples (tMn) were stabilized by acidification acidification with Optima grade nitric acid to a pH of &lt;2 and stored at 4 degrees C until analysis. All shipboard manipulations were performed in a laminar flow hood with clean techniques. Mn concentrations were determined on a Thermoquest Finnigan Element 2 double focusing, single collector, magnetic sector inductively coupled plasma mass spectrometer (ICP-MS) at the SIO unified laboratory analytical facility. ICP-MS was done at low resolution following instrument and induction parameters described previously (Field et al., 1999). Samples were diluted 1:50 in 2% nitric acid in quartz-distilled (QD) water prior to analysis. A calibration curve was prepared as described previously (Rodushkin and Ruth, 1998) using matrix-matched external standards made with 2% natural seawater stripped of metals by precipitation with Optima ammonium hydroxide. Indium (1 ppb) was used as an internal standard in all standards and samples. Standard additions (Willard et al., 1965) were used to rule out a matrix effect. To confirm analytical accuracy, reference waters CASS-4 and NASS-5 (Verplank et al., 2001) were included in the analysis as samples. Our experimentally determined average Mn concentration for CASS was 56 ± 10 nM (reported to be 51 nM) and for NASS-5 it was16 ± 8 nM (reported to be 17 nM). Six samples from station 1 were collected, processed and analyzed in duplicate. The average standard deviation was 8 nM, which includes variation due to both sampling and analytical error.</p>
Specified by the Principal Investigator(s)
<p>BCO-DMO processing:<br />
- modified parameter names to conform with BCO-DMO naming conventions;<br />
- formatted date to mm/dd/yyyy; added separate month, day, and year columns;<br />
- converted lat and lon to decimal degrees.</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
CTD Sea-Bird
CTD Sea-Bird
PI Supplied Instrument Name: CTD Sea-Bird PI Supplied Instrument Description:Hydrothermal plumes were detected by turbidity anomalies as measured by an air-calibrated transmissometer (WetLabs) on a CTD rosette (Sea-Bird). Water samples were collected in 10-l niskin bottles by CTD Rosette (Sea-Bird). Instrument Name: CTD Sea-Bird Instrument Short Name:CTD Sea-Bird Instrument Description: A Conductivity, Temperature, Depth (CTD) sensor package from SeaBird Electronics. This instrument designation is used when specific make and model are not known or when a more specific term is not available in the BCO-DMO vocabulary. Refer to the dataset-specific metadata for more information about the specific CTD used. More information from: http://www.seabird.com/ Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/130/
Thermoquest Finnigan Element 2
Thermoquest Finnigan Element 2
PI Supplied Instrument Name: Thermoquest Finnigan Element 2 PI Supplied Instrument Description:Mn concentrations were determined on a Thermoquest Finnigan Element 2 double focusing, single collector, magnetic sector inductively coupled plasma mass spectrometer (ICP-MS) at the SIO unified laboratory analytical facility. Instrument Name: Inductively Coupled Plasma Mass Spectrometer Instrument Short Name:ICP Mass Spec Instrument Description: An ICP Mass Spec is an instrument that passes nebulized samples into an inductively-coupled gas plasma (8-10000 K) where they are atomized and ionized. Ions of specific mass-to-charge ratios are quantified in a quadrupole mass spectrometer. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB15/
Niskin bottle
Niskin bottle
PI Supplied Instrument Name: Niskin bottle PI Supplied Instrument Description:Water samples were collected in 10-l niskin bottles by CTD Rosette (Sea-Bird). Samples were transferred from niskin bottles to acidwashed 50 ml polypropylene tubes. Instrument Name: Niskin bottle Instrument Short Name:Niskin bottle Instrument Description: A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/
Transmissometer
Transmissometer
PI Supplied Instrument Name: Transmissometer PI Supplied Instrument Description:Hydrothermal plumes were detected by turbidity anomalies as measured by an air-calibrated transmissometer (WetLabs) on a CTD rosette (Sea-Bird). Instrument Name: Transmissometer Instrument Short Name:Transmissometer Instrument Description: A transmissometer measures the beam attenuation coefficient of the lightsource over the instrument's path-length. This instrument designation is used when specific manufacturer, make and model are not known. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/124/
Cruise: GoCAL1
GoCAL1
R/V New Horizon
Community Standard Description
International Council for the Exploration of the Sea
R/V New Horizon
vessel
GoCAL1
Brian N. Popp
University of Hawai'i
Cruise: GoCAL2
GoCAL2
R/V New Horizon
Community Standard Description
International Council for the Exploration of the Sea
R/V New Horizon
vessel
GoCAL2
Brian N. Popp
University of Hawai'i
Cruise: GoCAL3
GoCAL3
R/V New Horizon
Community Standard Description
International Council for the Exploration of the Sea
R/V New Horizon
vessel
GoCAL3
Brian N. Popp
University of Hawai'i
R/V New Horizon
Community Standard Description
International Council for the Exploration of the Sea
R/V New Horizon
vessel