http://lod.bco-dmo.org/id/dataset/986669
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
2025-10-13
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Porewater geochemical data from sediment pushcores collected from Southern California Seeps in July 2023 on R/V Atlantis cruise AT50-12
2025-11-24
publication
2025-11-24
revision
BCO-DMO Linked Data URI
2025-11-24
creation
http://lod.bco-dmo.org/id/dataset/986669
Shana Goffredi
Occidental College
principalInvestigator
Victoria J. Orphan
California Institute of Technology
principalInvestigator
John S. Magyar
California Institute of Technology
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: Magyar, J. S., Orphan, V. J., Goffredi, S. (2025) Porewater geochemical data from sediment pushcores collected from Southern California Seeps in July 2023 on R/V Atlantis cruise AT50-12. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-11-24 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/986669 [access date]
AT50-12 IC Data Dataset Description: Methods and Sampling: <p>Sediment pushcores were collected by deep-submergence vehicle (DSV) Alvin from the R/V Atlantis in July 2023 (cruise ID AT50-12) at La Jolla Reef (32.8135, -117.4081), Del Mar Seep (32.9043, -117.7824), Santa Monica Seep Mound 800 (33.7993, -118.6465), Santa Monica Seep Mound 863 (33.7891, -118.6683), Qupé Seep (Redondo Knoll) (33.6505, -118.5522), and Palos Verdes Seep (33.6993, -118.3766). Pushcores were manually sectioned into 1 or 3 centimeter (cm) horizons using plastic rings, and porewaters were extracted using a KC Denmark squeezer. Samples for ion chromatography were frozen shipboard and thawed immediately prior to analysis. Measurements were made using a Thermo Dual Dionex Integrion HPIC ion chromatography system with either a 250 millimeter (mm) Dionex IonPac AS19-4 micrometer (um) column (anions) with 50 mm guard column or a 250 mm Dionex IonPac CS16-4um column (cations) with a 50 mm guard column, in the Resnick Water and Environment Laboratory at the California Institute of Technology (Caltech).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2048666 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2048666
onGoing
Shana Goffredi
Occidental College
323-259-1470
1600 Campus Road
Los Angeles
CA
90041-3314
USA
sgoffredi@oxy.edu
pointOfContact
Victoria J. Orphan
California Institute of Technology
626-395-1786
109A North Mudd MC 100-23
Pasadena
CA
91125
USA
vorphan@caltech.edu
pointOfContact
John S. Magyar
California Institute of Technology
626-395-6271
116 North Mudd MC 100-23
Pasadena
CA
91125
USA
jmagyar@caltech.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
serial
Fluoride
Acetate
Formate
Chloride
Bromide
Nitrate
Sulfate
Thiosulfate
Phosphate
Lithium
Sodium
Ammonium
Potassium
Magnesium
Calcium
pH
Dive
Lat
Long
Horizon
Date_UTC
Time_UTC
Depth_m
Station
Sample_Name
DSV Alvin
Thermo Dual Dionex Integrion HPIC ion chromatography system
KC Denmark squeezer
theme
None, User defined
sample identification
fluoride_ion
acetate
formate
chloride
bromides
Nitrate
sulfate
S2O3
phosphate
Lithium
Sodium
Ammonium
potassium
Magnesium
Calcium
pH
dive_id
latitude
longitude
depth core
date
time of day
depth_w
station
featureType
BCO-DMO Standard Parameters
HOV Alvin
Ion Chromatograph
KC Pore-Water Pressing Bench
instrument
BCO-DMO Standard Instruments
AT50-12
service
Deployment Activity
Southern California Borderland
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.
Collaborative Research: Redefining the footprint of deep ocean methane seepage for benthic ecosystems
https://osprey.bco-dmo.org/project/840220
Collaborative Research: Redefining the footprint of deep ocean methane seepage for benthic ecosystems
<p><em>NSF Award Abstract:</em><br />
This research examines the role of deep-sea organisms in determining the fate and footprint of methane, a potent greenhouse gas, on Pacific continental margins. The investigators are evaluating the deep ocean methanosphere defined by the microbial communities that consume methane and the animals that directly feed on or form symbioses with methane-consuming microbes. They are also investigating animal communities that gain energy indirectly from methane, as well as those that take advantage of carbonate rocks, the physical manifestation of methane consumption in seafloor sediments. The study of methane seeps in the deep waters of both Alaska (4400-5500 meters) and Southern California (450-1040 meters) is enabling comparisons of the methanosphere under different food-limitation and oxygen regimes. By applying diverse chemical, isotopic, microscopy, and genetic-based analyses to seep microbes and fauna, this study is advancing understanding of the contribution of methane to deep-sea biodiversity and ecosystem function, information that can inform management and conservation actions in US waters. In addition to training for graduate and undergraduate students at their home institutions, the investigators are collaborating with the Alaska Native Science and Engineering Program (ANSEP). They are recruiting Alaskan undergraduates to participate in the research, contributing to ANSEP's online resources that promote interaction between scientists and middle and high school students, and participating in ANSEP's annual residential Career Exploration in Marine Science programs to engage middle school students in learning about deep-sea ecosystems and the variety of career pathways available in marine related fields.</p>
<p>Microbial production and consumption of methane is dynamic and widespread along continental margins, and some animals within deep-sea methane seeps rely on the oxidation and sequestration of methane for nutrition. At the same time, understanding of methane-dependent processes and symbioses in the deep-sea environment is still rudimentary. The goals of this study are to 1) examine the diversity of animals involved in methane-based symbioses and heterotrophic consumption of methane-oxidizing microbes and how these symbioses extend the periphery of seeps, contributing to non-seep, continental slope food webs; and 2) determine whether carbonates on the seep periphery sustain active methanotrophic microbial assemblages, providing a localized food source or chemical fuel for thiotrophic symbioses, via anaerobic oxidation of methane, or free-living, sulfide-oxidizing bacteria consumed by animals. The investigators are addressing these goals by surveying, sampling, and characterizing microbes, water, sediments, carbonates and animals at a deep seep site on the Aleutian Margin and a shallow site off Southern California. Shipboard experiments and laboratory analyses are using molecular, isotopic, geochemical, and radiotracer tools to understand transfer of methane-sourced carbon from aerobic methanotrophs under multiple oxygen levels, pressures, and photosynthetic food inputs. This approach offers a wide lens by which to examine the methane seep footprint, allow reinterpretation of past observations, and identify new scientific areas for future study. Improved characterization of the deep continental margin methanosphere informs climate science, biodiversity conservation, and resource management.</p>
Methanosphere
largerWorkCitation
project
eng; USA
oceans
Southern California Borderland
-118.6471938
-117.40811
32.813523
33.79968797
2023-07-16
2023-07-27
Gulf of Alaska and Southern California Bight
0
BCO-DMO catalogue of parameters from Porewater geochemical data from sediment pushcores collected from Southern California Seeps in July 2023 on R/V Atlantis cruise AT50-12
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/989398.rdf
Name: serial
Units: unitless
Description: <p>Internal Orphan Lab identifier (sample serial number)</p>
http://lod.bco-dmo.org/id/dataset-parameter/989399.rdf
Name: Fluoride
Units: millimolar (mM)
Description: <p>concentration of fluoride ion</p>
http://lod.bco-dmo.org/id/dataset-parameter/989400.rdf
Name: Acetate
Units: millimolar (mM)
Description: <p>concentration of acetate ion</p>
http://lod.bco-dmo.org/id/dataset-parameter/989401.rdf
Name: Formate
Units: millimolar (mM)
Description: <p>concentration of formate ion</p>
http://lod.bco-dmo.org/id/dataset-parameter/989402.rdf
Name: Chloride
Units: millimolar (mM)
Description: <p>concentration of chloride ion</p>
http://lod.bco-dmo.org/id/dataset-parameter/989403.rdf
Name: Bromide
Units: millimolar (mM)
Description: <p>concentration of bromide ion</p>
http://lod.bco-dmo.org/id/dataset-parameter/989404.rdf
Name: Nitrate
Units: millimolar (mM)
Description: <p>concentration of nitrate ion</p>
http://lod.bco-dmo.org/id/dataset-parameter/989405.rdf
Name: Sulfate
Units: millimolar (mM)
Description: <p>concentration of sulfate ion</p>
http://lod.bco-dmo.org/id/dataset-parameter/989406.rdf
Name: Thiosulfate
Units: millimolar (mM)
Description: <p>concentration of thiosulfate ion</p>
http://lod.bco-dmo.org/id/dataset-parameter/989407.rdf
Name: Phosphate
Units: millimolar (mM)
Description: <p>concentration of phosphate ion</p>
http://lod.bco-dmo.org/id/dataset-parameter/989408.rdf
Name: Lithium
Units: millimolar (mM)
Description: <p>concentration of lithium ion</p>
http://lod.bco-dmo.org/id/dataset-parameter/989409.rdf
Name: Sodium
Units: millimolar (mM)
Description: <p>concentration of sodium ion</p>
http://lod.bco-dmo.org/id/dataset-parameter/989410.rdf
Name: Ammonium
Units: millimolar (mM)
Description: <p>concentration of ammonium ion</p>
http://lod.bco-dmo.org/id/dataset-parameter/989411.rdf
Name: Potassium
Units: millimolar (mM)
Description: <p>concentration of potassium ion</p>
http://lod.bco-dmo.org/id/dataset-parameter/989412.rdf
Name: Magnesium
Units: millimolar (mM)
Description: <p>concentration of magnesium ion</p>
http://lod.bco-dmo.org/id/dataset-parameter/989413.rdf
Name: Calcium
Units: millimolar (mM)
Description: <p>concentration of calcium ion</p>
http://lod.bco-dmo.org/id/dataset-parameter/989414.rdf
Name: pH
Units: unitless
Description: <p>pH value, measured shipboard</p>
http://lod.bco-dmo.org/id/dataset-parameter/989415.rdf
Name: Dive
Units: unitless
Description: <p>Dive Number, DSV Alvin</p>
http://lod.bco-dmo.org/id/dataset-parameter/989416.rdf
Name: Lat
Units: decimal degrees
Description: <p>Latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/989417.rdf
Name: Long
Units: decimal degrees
Description: <p>Longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/989418.rdf
Name: Horizon
Units: centimeters (cm)
Description: <p>Depth (cm) in sediment, measured from top of core</p>
http://lod.bco-dmo.org/id/dataset-parameter/989419.rdf
Name: Date_UTC
Units: unitless
Description: <p>Core collection date (UTC)</p>
http://lod.bco-dmo.org/id/dataset-parameter/989420.rdf
Name: Time_UTC
Units: unitless
Description: <p>Core collection time (UTC)</p>
http://lod.bco-dmo.org/id/dataset-parameter/989421.rdf
Name: Depth_m
Units: meters (m)
Description: <p>ocean depth in meters at the sampling location</p>
http://lod.bco-dmo.org/id/dataset-parameter/989422.rdf
Name: Station
Units: unitless
Description: <p>name of the sampling site</p>
http://lod.bco-dmo.org/id/dataset-parameter/989423.rdf
Name: Sample_Name
Units: unitless
Description: <p>the sample name, which is composed of the dive number and the DSV pushcore number</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
https://osprey.bco-dmo.org/dataset/986669/data/download
download
onLine
dataset
<p>Sediment pushcores were collected by deep-submergence vehicle (DSV) Alvin from the R/V Atlantis in July 2023 (cruise ID AT50-12) at La Jolla Reef (32.8135, -117.4081), Del Mar Seep (32.9043, -117.7824), Santa Monica Seep Mound 800 (33.7993, -118.6465), Santa Monica Seep Mound 863 (33.7891, -118.6683), Qupé Seep (Redondo Knoll) (33.6505, -118.5522), and Palos Verdes Seep (33.6993, -118.3766). Pushcores were manually sectioned into 1 or 3 centimeter (cm) horizons using plastic rings, and porewaters were extracted using a KC Denmark squeezer. Samples for ion chromatography were frozen shipboard and thawed immediately prior to analysis. Measurements were made using a Thermo Dual Dionex Integrion HPIC ion chromatography system with either a 250 millimeter (mm) Dionex IonPac AS19-4 micrometer (um) column (anions) with 50 mm guard column or a 250 mm Dionex IonPac CS16-4um column (cations) with a 50 mm guard column, in the Resnick Water and Environment Laboratory at the California Institute of Technology (Caltech).</p>
Specified by the Principal Investigator(s)
<p>100 microliter (uL) samples are diluted 50x in milliQ nanopure water before running. Standard curves are generated using calibration standards diluted similarly to samples, with 100 uL of 500 millimolar (mM) NaCl added to mimic typical seawater sample peak behavior. Analyte peaks are integrated and values are calculated using the standards automatically in the Chromeleon software, with manual QC to ensure regular peak shapes.</p>
Specified by the Principal Investigator(s)
- Imported original file "AT50-12_IC_all_forsubmission_20250414.csv" into the BCO-DMO system.
- Marked "n.a.", "NOT MEASURED", and "NOT_MEASURED" as missing data values (missing data are empty/blank in the final CSV file).
- Replaced non-standard character "é" with "e" in the "Station" column.
- Converted "Date_UTC" column to YYYY-MM-DD format.
- Removed the empty "NOT_MEASURED" column.
- Saved the final file as "986669_v1_at50-12_ic_data.csv".
Specified by BCO-DMO Data Managers
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
DSV Alvin
DSV Alvin
PI Supplied Instrument Name: DSV Alvin PI Supplied Instrument Description:DSV Alvin is owned by the U. S. Navy and operated for NSF by the Woods Hole Oceanographic Institution (WHOI). DSV Alvin is capable of diving to 6500 meters (about 4 miles). The R/V Atlantis is the support vessel for Alvin. For a complete description see: https://www.whoi.edu/what-we-do/explore/underwater-vehicles/hov-alvin/ Instrument Name: HOV Alvin Instrument Short Name: Instrument Description: Human Occupied Vehicle (HOV) Alvin is part of the National Deep Submergence Facility (NDSF). Alvin enables in-situ data collection and observation by two scientists to depths reaching 6,500 meters, during dives lasting up to ten hours.
Commissioned in 1964 as one of the world’s first deep-ocean submersibles, Alvin has remained state-of-the-art as a result of numerous overhauls and upgrades made over its lifetime. The most recent upgrades, begun in 2011 and completed in 2021, saw the installation of a new, larger personnel sphere with a more ergonomic interior; improved visibility and overlapping fields of view; longer bottoms times; new lighting and high-definition imaging systems; improved sensors, data acquisition and download speed. It also doubled the science basket payload, and improved the command-and-control system allowing greater speed, range and maneuverability.
With seven reversible thrusters, it can hover in the water, maneuver over rugged topography, or rest on the sea floor. It can collect data throughout the water column, produce a variety of maps and perform photographic surveys. Alvin also has two robotic arms that can manipulate instruments, obtain samples, and its basket can be reconfigured daily based on the needs of the upcoming dive.
Alvin's depth rating of 6,500m gives researchers in-person access to 99% of the ocean floor. Alvin is a proven and reliable platform capable of diving for up to 30 days in a row before requiring a single scheduled maintenance day. Recent collaborations with autonomous vehicles such as Sentry have proven extremely beneficial, allowing PIs to visit promising sites to collect samples and data in person within hours of their being discovered, and UNOLs driven technological advances have improved the ability for scientific outreach and collaboration via telepresence
Alvin is named for Allyn Vine, a WHOI engineer and geophysicist who helped pioneer deep submergence research and technology.
(from https://www.whoi.edu/what-we-do/explore/underwater-vehicles/hov-alvin/, accessed 2022-09-09)
Thermo Dual Dionex Integrion HPIC ion chromatography system
Thermo Dual Dionex Integrion HPIC ion chromatography system
PI Supplied Instrument Name: Thermo Dual Dionex Integrion HPIC ion chromatography system PI Supplied Instrument Description:Thermo Dual Dionex Integrion HPIC ion chromatography system with either a 250 mm Dionex IonPac AS19-4um column (anions) with 50 mm guard column or a 250 mm Dionex IonPac CS16-4um column (cations) with a 50 mm guard column, in the Resnick Water and Environment Laboratory at the California Institute of Technology (Caltech). 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)
KC Denmark squeezer
KC Denmark squeezer
PI Supplied Instrument Name: KC Denmark squeezer PI Supplied Instrument Description:Porewaters were extracted using a KC Denmark squeezer. Instrument Name: KC Pore-Water Pressing Bench Instrument Short Name: Instrument Description: The KC Pore-water pressing bench, made by KC Denmark Research Equipment, allows pore-water extraction of any kind of sediments, from sediments rich in organic material, to sandy sediments. Sediment cores are segmented and placed in the pressing house, which is closed by means of the handle on top of the house. An over-pressure is applied (fed-in) at the reduction valve and the valves of the houses in operation are opened. The resulting compression of the sediment matrix leads to expelling of the pore-water, which is sampled in containers beneath the pressing house. Operation in a glove bag prevents atmospheric contamination with, for example, oxygen, so anaerobic analysis of the pore-water is possible. The standard cylinders are made from black Polyoxymethylene (POM). However, the cylinders and all accessories are also available as AISI 316 stainless steel for special purposes. The pressing bench consists of 5 pressing houses, each 100 ml. They can hold a maximum sample diameter of 40 mm. The instrument has a maximum operating pressure of 4 bar (400 kPa).
Cruise: AT50-12
AT50-12
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
AT50-12
Lisa A. Levin
University of California-San Diego Scripps
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel