http://lod.bco-dmo.org/id/dataset/863144
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
2021-10-13
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Sediment C isotope ratios from incubations amended with 13C-labeled substrates from samples collected on cruise OC1703A aboard R/V Oceanus and cruise AT36 aboard R/V Atlantis
2021-10-13
publication
2021-10-13
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2022-04-11
publication
https://doi.org/10.26008/1912/bco-dmo.863144.1
Anne E. Dekas
Stanford University
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
documentDigital
Cite this dataset as: Dekas, A. E. (2021) Sediment C isotope ratios from incubations amended with 13C-labeled substrates from samples collected on cruise OC1703A aboard R/V Oceanus and cruise AT36 aboard R/V Atlantis. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-10-13 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.863144.1 [access date]
OC1703A and AT36 sediment C isotope ratios Dataset Description: Acquisition Description: <p>Sediment cores were collected in the northwest Pacific Ocean off the coast of San Francisco, CA on the R/V Oceanus during cruise OC1703A in March 2017 and in the northeast Atlantic off the coast of Woods Hole, MA on the R/V Atlantis during cruise AT36 in July 2016. Sediment cores in the northwest Pacific were 15–30 cm long and collected at five sites (100–4475 water depths) using an MC-800 multicore (Ocean Instruments). Sediment cores in the northeast Atlantic were 15 cm long and collected at two sites (1252–1496 water depth) using an MC-400 multicore (Ocean Instruments). Both multicores were modified with Go-Pro cameras in custom pressure housing to provide real-time video feeds and guide sampling (MISO Facility, Woods Hole Oceanographic Institute). Cores were stored at 4ºC for ≤24 hours until they were sectioned on board in 2.5, 3, or 5 cm depth increments.</p>
<p>Sediment from two cores at each of the five Pacific sampling sites was sectioned in 5 cm intervals (3–5 sections per core) and mixed with 0.2 µm-filtered, argon-sparged bottom water (1:1–1:2 ratio of sediment to seawater). About 60 mL of sediment slurry was aliquoted into each 120 mL glass serum bottle, sealed with NaOH pre-treated black butyl rubber stoppers (Geo-microbial technologies, Ochelata, OK, USA) and aluminum crimp caps, and the headspace exchanged using argon. Incubations from each sediment depth were amended with ¹⁵N-ammonium (final concentration: 500 µM; Cambridge Isotopes, NLM-467-5, Lot I-19633L), ¹³C-glucose (50 µM; Cambridge Isotopes, CLM-1396-1, Lot PR-27921), ¹³C-bicarbonate (final concentration 1.15 mM; Cambridge Isotopes, CLM-441-5, Lot PR-27797), or 5 mL of ¹⁵N₂ (Cambridge Isotopes, NLM-363-PK, Lot I-19197). ¹⁵N₂ gas was passed through an acid trap before addition to incubation bottles to scavenge any undetected contaminants. Select ¹⁵N-ammonium and ¹³C-glucose incubations were additionally amended with non-isotope labeled glucose (50 µM) and ammonium (500 µM), respectively. Incubations were over-pressured to 30 psi using argon. All incubations were conducted in duplicate, with the exception of the ¹⁵N₂ incubations, which were conducted in triplicate. All Pacific incubations were subsampled at 2, 4, 8, and 12 weeks for bulk C or N stable isotope analysis.</p>
<p>For the Atlantic samples, cores were sectioned into 3 cm sediment horizons and stored under anaerobic conditions at 4ºC for 3 months. Incubation set up was the same as for the Pacific samples, except only 20 mL of slurry was aliquoted into each 60 mL serum bottle and they were sealed with blue butyl rubber stoppers (Bellco Glass, Vineland, NJ, USA). All incubations were amended with ¹⁵N-ammonium (final concentration: 1 mM; Cambridge Isotopes, NLM-467-5, Lot I-19633L) or 5 mL ¹⁵N₂ (Cambridge Isotopes, NLM-363-PK, Lot I-19197) and incubations were subsampled at 0 and 30 days. A total of nearly 300 incubations of Pacific and Atlantic sediment were prepared.</p>
<p>Sediment slurries were subsampled with a needle and syringe and sampled slurry was immediately centrifuged at 4,000 x g for 30 seconds. The supernatant was removed and stored at -20ºC, and the sediment pellet frozen at -20ºC. For incubations amended with ¹⁵N-ammonium, sediment pellets were washed three times with PBS and KCl after defrosting and before drying as previously described (Dekas et al., 2014). Briefly, 1 x PBS was added to sediment pellets, vortexed, centrifuged at 15,100 x g for 15 min, the supernatant removed, and repeated with 2M KCl (incubated at 1 h at room temperature) and then 1 x PBS. For incubations amended with ¹³C-glucose and ¹³C-bicarbonate, sediment pellets were also washed, but we replaced the KCl incubation with another 1 x PBS wash step. Sediment pellets were dried overnight at 60ºC and left to equilibrate to ambient humidity for at least three days. For N isotope analysis, samples were weighed into tin capsules. For C isotope analysis, samples were weighed into silver capsules and acid fumigated to remove carbonates as previously described (Harris et al., 2001). Acid fumigated samples were then encapsulated into tin capsules. All samples were analyzed using Elementar Vario EL Cube or Micro Cube elemental analyzer (Elementar Analysensysteme GmbH, Hanau, Germany) interfaced to either an Isoprime VisION IRMS (Elementar UK Ltd, Cheadle, UK) or a PDZ Europa 20-20 isotope ratio mass spectrometer (Sercon Ltd., Cheshire, UK) at UC Davis Stable Isotope Facility. They report a long term deviation of 0.2‰ for ¹³C and 0.3‰ for ¹⁵N.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1634297 Award URL: http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1634297
completed
Anne E. Dekas
Stanford University
650-736-1225
473 Via Ortega, Y2E2 Room 140
Stanford
CA
94305-4216
USA
dekas@stanford.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Cruise
ISO_Date_Local
Latitude
Longitude
Deployment
Water_Depth_m
Core
Depth_cm
Sample_ID
d13C
C_amount_micrograms
Sediment_weight_mg
Time_point_weeks
Amendment
Isoprime VisION IRMS
DZ Europa 20-20 isotope ratio mass spectrometer
Go-Pro cameras in custom pressure housing
MC-800 multicore (Ocean Instruments)
MC-400 multicore (Ocean Instruments)
Elementar Vario EL Cube or Micro Cube elemental analyzer
theme
None, User defined
cruise id
date
latitude
longitude
deployment number
depth
core id
depth core
sample identification
d13C
Elemental carbon (C)
weight
time_point
treatment
featureType
BCO-DMO Standard Parameters
Isotope-ratio Mass Spectrometer
Isotope-ratio Mass Spectrometer
Camera
Multi Corer
Multi Corer
Elemental Analyzer
instrument
BCO-DMO Standard Instruments
OC1703A
AT36
service
Deployment Activity
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.
Nitrogen Fixation in Deep-Sea Sediments
https://www.bco-dmo.org/project/710001
Nitrogen Fixation in Deep-Sea Sediments
<p><em>NSF Award Abstract:</em><br />
Life requires nitrogen for growth. Atmospheric nitrogen (N2) is the most abundant form of nitrogen on the surface of the planet, but most organisms cannot assimilate N2 directly. Habitats can therefore be nitrogen limited, meaning the demand for "bioavailable" nitrogen exceeds the supply, and its availability controls the overall growth and productivity of the community. A small subset of microorganisms, termed diazotrophs, convert N2 to bioavailable forms of nitrogen, including ammonium and nitrogenous organic matter, in a process known as N2 fixation. Diazotrophs are the largest natural source of bioavailable nitrogen on the planet, and the rate at which they fix N2 can control the rates at which other important microbial processes occur, such as the production and consumption of greenhouse gases. Understanding diazotrophs in the environment - their identity, distribution, activity levels, and biogeochemical controls - is therefore essential to understanding overall microbial community activity and biogeochemical cycling. The goal of this project is to characterize N2 fixation in deep-sea sediments, a generally understudied but expansive habitat, covering nearly two thirds of our planet. The project will have broader impacts via educational outreach, support and training of early career scientists, and scientific impact: since rates of marine methane, carbon dioxide, and nitrous oxide cycling are affected by nitrogen availability, the results will inform our understanding of greenhouse gas cycling in the marine environment, and therefore climate stability, a topic central to global security.</p>
<p>N2 fixation is a critical and intensely studied metabolism in the marine photic zone. Much less is known about N2 fixation in deep-sea sediments, but it could be an important factor in both benthic productivity and ocean-scale elemental cycling. Several observations have suggested or directly detected N2 fixation at localized areas of enhanced productivity on the seafloor (e.g., methane seeps and hydrothermal vents), raising the possibility that deep-sea N2 fixation is widespread. However, few measurements of N2 fixation have been made outside of these anomalous areas, and thus little is known about N2 fixation in the vast majority of the deep ocean floor. Preliminary data suggest N2 fixation does occur in typical deep marine sediment, and is mediated by a diverse set of yet unidentified microorganisms. This project will combine techniques from molecular biology and geochemistry to systematically investigate N2 fixation in representative deep-sea sediments collected along a depth profile (500 to 4500 m water depth) offshore California. The project will determine the (1) rates and distribution of N2 fixation (2) abundance, diversity, and distribution of genes and transcripts associated with N2 fixation (nif) (3) phylogenetic identity of the biological mediators (diazotrophs) and (4) physiochemical controls on diazotrophic community structure and activity. For context, the activity of the non-diazotrophic bacterial community will also be characterized. The results may lead to upward revisions of the estimates of new nitrogen production in the seafloor, and therefore change our understanding of the current balance of the marine nitrogen cycle. Together, this hypothesis-driven characterization of N2 fixation in deep-sea sediments will shed light on an expansive, climatically important, and traditionally understudied habitat, and facilitate more accurate extrapolation of the rates and distribution of N2 fixation on the whole seafloor as well as the metabolic response of the seafloor community to environmental change.</p>
Deep Sediment N Fix
largerWorkCitation
project
eng; USA
oceans
-124.92211
-122.544233
35.68905
37.1343783
2017-03-14
2017-03-21
California Shelf (36,-123)
0
BCO-DMO catalogue of parameters from Sediment C isotope ratios from incubations amended with 13C-labeled substrates from samples collected on cruise OC1703A aboard R/V Oceanus and cruise AT36 aboard R/V Atlantis
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/863174.rdf
Name: Cruise
Units: unitless
Description: Cruise ID number
http://lod.bco-dmo.org/id/dataset-parameter/863175.rdf
Name: ISO_Date_Local
Units: unitless
Description: Sampling date (local) in format YYYY-MM-DD
http://lod.bco-dmo.org/id/dataset-parameter/863176.rdf
Name: Latitude
Units: decimal degrees North
Description: Sampling latitude
http://lod.bco-dmo.org/id/dataset-parameter/863177.rdf
Name: Longitude
Units: decimal degrees East
Description: Sampling longitude
http://lod.bco-dmo.org/id/dataset-parameter/863178.rdf
Name: Deployment
Units: unitless
Description: Deployment number
http://lod.bco-dmo.org/id/dataset-parameter/863179.rdf
Name: Water_Depth_m
Units: meters (m)
Description: Sampling water depth
http://lod.bco-dmo.org/id/dataset-parameter/863180.rdf
Name: Core
Units: unitless
Description: Multicore number
http://lod.bco-dmo.org/id/dataset-parameter/863181.rdf
Name: Depth_cm
Units: centimeters (cm)
Description: Sampling sediment depth
http://lod.bco-dmo.org/id/dataset-parameter/863182.rdf
Name: Sample_ID
Units: unitless
Description: Sample ID number
http://lod.bco-dmo.org/id/dataset-parameter/863183.rdf
Name: d13C
Units: permil
Description: Delta 13C isotope ratio
http://lod.bco-dmo.org/id/dataset-parameter/863184.rdf
Name: C_amount_micrograms
Units: micrograms (ug)
Description: Amount of carbon
http://lod.bco-dmo.org/id/dataset-parameter/863185.rdf
Name: Sediment_weight_mg
Units: milligrams (mg)
Description: Sediment weight
http://lod.bco-dmo.org/id/dataset-parameter/863186.rdf
Name: Time_point_weeks
Units: weeks
Description: Subsample time point
http://lod.bco-dmo.org/id/dataset-parameter/863187.rdf
Name: Amendment
Units: unitless
Description: Label amendment
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://www.bco-dmo.org/dataset/863144/data/download
download
onLine
dataset
<p>Sediment cores were collected in the northwest Pacific Ocean off the coast of San Francisco, CA on the R/V Oceanus during cruise OC1703A in March 2017 and in the northeast Atlantic off the coast of Woods Hole, MA on the R/V Atlantis during cruise AT36 in July 2016. Sediment cores in the northwest Pacific were 15–30 cm long and collected at five sites (100–4475 water depths) using an MC-800 multicore (Ocean Instruments). Sediment cores in the northeast Atlantic were 15 cm long and collected at two sites (1252–1496 water depth) using an MC-400 multicore (Ocean Instruments). Both multicores were modified with Go-Pro cameras in custom pressure housing to provide real-time video feeds and guide sampling (MISO Facility, Woods Hole Oceanographic Institute). Cores were stored at 4ºC for ≤24 hours until they were sectioned on board in 2.5, 3, or 5 cm depth increments.</p>
<p>Sediment from two cores at each of the five Pacific sampling sites was sectioned in 5 cm intervals (3–5 sections per core) and mixed with 0.2 µm-filtered, argon-sparged bottom water (1:1–1:2 ratio of sediment to seawater). About 60 mL of sediment slurry was aliquoted into each 120 mL glass serum bottle, sealed with NaOH pre-treated black butyl rubber stoppers (Geo-microbial technologies, Ochelata, OK, USA) and aluminum crimp caps, and the headspace exchanged using argon. Incubations from each sediment depth were amended with ¹⁵N-ammonium (final concentration: 500 µM; Cambridge Isotopes, NLM-467-5, Lot I-19633L), ¹³C-glucose (50 µM; Cambridge Isotopes, CLM-1396-1, Lot PR-27921), ¹³C-bicarbonate (final concentration 1.15 mM; Cambridge Isotopes, CLM-441-5, Lot PR-27797), or 5 mL of ¹⁵N₂ (Cambridge Isotopes, NLM-363-PK, Lot I-19197). ¹⁵N₂ gas was passed through an acid trap before addition to incubation bottles to scavenge any undetected contaminants. Select ¹⁵N-ammonium and ¹³C-glucose incubations were additionally amended with non-isotope labeled glucose (50 µM) and ammonium (500 µM), respectively. Incubations were over-pressured to 30 psi using argon. All incubations were conducted in duplicate, with the exception of the ¹⁵N₂ incubations, which were conducted in triplicate. All Pacific incubations were subsampled at 2, 4, 8, and 12 weeks for bulk C or N stable isotope analysis.</p>
<p>For the Atlantic samples, cores were sectioned into 3 cm sediment horizons and stored under anaerobic conditions at 4ºC for 3 months. Incubation set up was the same as for the Pacific samples, except only 20 mL of slurry was aliquoted into each 60 mL serum bottle and they were sealed with blue butyl rubber stoppers (Bellco Glass, Vineland, NJ, USA). All incubations were amended with ¹⁵N-ammonium (final concentration: 1 mM; Cambridge Isotopes, NLM-467-5, Lot I-19633L) or 5 mL ¹⁵N₂ (Cambridge Isotopes, NLM-363-PK, Lot I-19197) and incubations were subsampled at 0 and 30 days. A total of nearly 300 incubations of Pacific and Atlantic sediment were prepared.</p>
<p>Sediment slurries were subsampled with a needle and syringe and sampled slurry was immediately centrifuged at 4,000 x g for 30 seconds. The supernatant was removed and stored at -20ºC, and the sediment pellet frozen at -20ºC. For incubations amended with ¹⁵N-ammonium, sediment pellets were washed three times with PBS and KCl after defrosting and before drying as previously described (Dekas et al., 2014). Briefly, 1 x PBS was added to sediment pellets, vortexed, centrifuged at 15,100 x g for 15 min, the supernatant removed, and repeated with 2M KCl (incubated at 1 h at room temperature) and then 1 x PBS. For incubations amended with ¹³C-glucose and ¹³C-bicarbonate, sediment pellets were also washed, but we replaced the KCl incubation with another 1 x PBS wash step. Sediment pellets were dried overnight at 60ºC and left to equilibrate to ambient humidity for at least three days. For N isotope analysis, samples were weighed into tin capsules. For C isotope analysis, samples were weighed into silver capsules and acid fumigated to remove carbonates as previously described (Harris et al., 2001). Acid fumigated samples were then encapsulated into tin capsules. All samples were analyzed using Elementar Vario EL Cube or Micro Cube elemental analyzer (Elementar Analysensysteme GmbH, Hanau, Germany) interfaced to either an Isoprime VisION IRMS (Elementar UK Ltd, Cheadle, UK) or a PDZ Europa 20-20 isotope ratio mass spectrometer (Sercon Ltd., Cheshire, UK) at UC Davis Stable Isotope Facility. They report a long term deviation of 0.2‰ for ¹³C and 0.3‰ for ¹⁵N.</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing:</strong><br />
- renamed fields to conform with BCO-DMO naming conventions;<br />
- replaced commas with semi-colons in the Core column;<br />
- removed apostrophes from the Depth_cm column;<br />
- converted longitude negative values to indicate West direction.</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
Isoprime VisION IRMS
Isoprime VisION IRMS
PI Supplied Instrument Name: Isoprime VisION IRMS Instrument Name: Isotope-ratio Mass Spectrometer Instrument Short Name:IR Mass Spec Instrument Description: The Isotope-ratio Mass Spectrometer is a particular type of mass spectrometer used to measure the relative abundance of isotopes in a given sample (e.g. VG Prism II Isotope Ratio Mass-Spectrometer). Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/
DZ Europa 20-20 isotope ratio mass spectrometer
DZ Europa 20-20 isotope ratio mass spectrometer
PI Supplied Instrument Name: DZ Europa 20-20 isotope ratio mass spectrometer Instrument Name: Isotope-ratio Mass Spectrometer Instrument Short Name:IR Mass Spec Instrument Description: The Isotope-ratio Mass Spectrometer is a particular type of mass spectrometer used to measure the relative abundance of isotopes in a given sample (e.g. VG Prism II Isotope Ratio Mass-Spectrometer). Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/
Go-Pro cameras in custom pressure housing
Go-Pro cameras in custom pressure housing
PI Supplied Instrument Name: Go-Pro cameras in custom pressure housing Instrument Name: Camera Instrument Short Name:camera Instrument Description: All types of photographic equipment including stills, video, film and digital systems. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/311/
MC-800 multicore (Ocean Instruments)
MC-800 multicore (Ocean Instruments)
PI Supplied Instrument Name: MC-800 multicore (Ocean Instruments) Instrument Name: Multi Corer Instrument Short Name:Multi Corer Instrument Description: The Multi Corer is a benthic coring device used to collect multiple, simultaneous, undisturbed sediment/water samples from the seafloor. Multiple coring tubes with varying sampling capacity depending on tube dimensions are mounted in a frame designed to sample the deep ocean seafloor. For more information, see Barnett et al. (1984) in Oceanologica Acta, 7, pp. 399-408. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/51/
MC-400 multicore (Ocean Instruments)
MC-400 multicore (Ocean Instruments)
PI Supplied Instrument Name: MC-400 multicore (Ocean Instruments) Instrument Name: Multi Corer Instrument Short Name:Multi Corer Instrument Description: The Multi Corer is a benthic coring device used to collect multiple, simultaneous, undisturbed sediment/water samples from the seafloor. Multiple coring tubes with varying sampling capacity depending on tube dimensions are mounted in a frame designed to sample the deep ocean seafloor. For more information, see Barnett et al. (1984) in Oceanologica Acta, 7, pp. 399-408. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/51/
Elementar Vario EL Cube or Micro Cube elemental analyzer
Elementar Vario EL Cube or Micro Cube elemental analyzer
PI Supplied Instrument Name: Elementar Vario EL Cube or Micro Cube elemental analyzer Instrument Name: Elemental Analyzer Instrument Short Name: Instrument Description: Instruments that quantify carbon, nitrogen and sometimes other elements by combusting the sample at very high temperature and assaying the resulting gaseous oxides. Usually used for samples including organic material. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB01/
Cruise: OC1703A
OC1703A
R/V Oceanus
Community Standard Description
International Council for the Exploration of the Sea
R/V Oceanus
vessel
OC1703A
Anne E. Dekas
Stanford University
Cruise: AT36
AT36
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
AT36
Anne E. Dekas
Stanford University
R/V Oceanus
Community Standard Description
International Council for the Exploration of the Sea
R/V Oceanus
vessel
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel