http://lod.bco-dmo.org/id/dataset/963407
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
2025-06-01
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Bacterial productivity of samples from three stations in the Western North Atlantic aboard R/V Atlantic Explorer cruise AE2413 during May 2024
2025-06-06
publication
2025-06-06
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2025-06-10
publication
https://doi.org/10.26008/1912/bco-dmo.963407.1
Carol Arnosti
University of North Carolina at Chapel Hill
principalInvestigator
Sherif Ghobrial
University of North Carolina at Chapel Hill
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: Ghobrial, S., Arnosti, C. (2025) Bacterial productivity of samples from three stations in the Western North Atlantic aboard R/V Atlantic Explorer cruise AE2413 during May 2024. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-06-06 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.963407.1 [access date]
AE2413 Bacterial productivity Dataset Description: Methods and Sampling: <p>Water for incubation &nbsp;was collected via Niskin bottles mounted on a rosette, equipped with a CTD. &nbsp;Bulk water was collected into an acid washed 50 mL Falcon tube directly from niskin bottles.&nbsp;</p>
<p>Isotopically diluted&nbsp;L-[3,4,5-3H(N)]-Leucine (Revvity, NET460250UC,&nbsp;specific activity of&nbsp;3.811 TBq/mmol) was added to 1.7ml triplicate subsamples and one TCA killed control&nbsp;(20 nM final concentration). &nbsp;Samples and killed control were&nbsp;incubated between 5 and 48 hours at nearly in-situ temperature or 4°C.&nbsp; Following incubation, live samples were killed with 100% (w/v) TCA and all samples were centrifuged (10,000 rpm at 4°C for 10 min) to pelletize cell material.&nbsp; The supernatant liquid was removed and 1 mL of ice cold 5% (w/v) TCA solution was added, followed by vortex mixing and centrifugation.&nbsp; Supernatant removal, mixing, and centrifugation were repeated using 1 mL of ice cold 80% ethanol solution.&nbsp; Again, the supernatant liquid was removed and each sample was left to dry in a hood overnight.&nbsp; After drying, 1 mL of scintillation cocktail (ScintiSafe 30% Cocktail, Fisher SX23-5) was added and left overnight&nbsp;so that&nbsp;precipitated proteins dissolve into scintillation fluid.&nbsp; Incorporated radioactivity was measured using a PerkinElmer Tri-Carb 2910TR LSA scintillation counter.&nbsp; Radioactivity was compared to 1 mL of scintillation cocktail spiked with an identical amount of&nbsp;isotopically diluted&nbsp;L-[3,4,5-3H(N)]-Leucine that was added to samples. &nbsp;Incorporation rate was calculated by dividing sample radioactivity by incubation time.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2241720 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2241720
completed
Carol Arnosti
University of North Carolina at Chapel Hill
919-962-5754
Dept. of Marine Sciences 3117A Venable/Murray Hall
Chapel Hill
NC
27599-3300
USA
arnosti@email.unc.edu
pointOfContact
Sherif Ghobrial
University of North Carolina at Chapel Hill
reef@unc.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
deployment
station
latitude_n
longitude_e
ISO_DateTime_UTC
date
time_local_est
cast_number
depth_description
depth_actual
insitu_temp
sample_type
incubation_type
incubation_pressure
incubation_temp
unamended_amended
substrate
incubation_time
DPM_Kill
DPM_rep1
DPM_rep2
DPM_rep3
Average_incorp
H3_Leu
stdev
CTD
PerkinElmer Tri-Carb 2910TR LSA scintillation counter
Niskin bottles
theme
None, User defined
Cruise identfier
station id
latitude
longitude
ISO_DateTime_UTC
date
time_local
cast
depth_comment
depth
water temperature at measurement depth
sample type
experiment type
water pressure
incubation or cultivation temperature (not ambient water temp)
sample description
incubation time or duration
radioactive_isotope_activity
mean
leucine incorporation rate
standard deviation of leucine incorporation rate
featureType
BCO-DMO Standard Parameters
CTD - profiler
Liquid Scintillation Counter
Niskin bottle
instrument
BCO-DMO Standard Instruments
AE2413
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.
Collaborative Research: Pressure effects on microbially-catalyzed organic matter degradation in the deep ocean
https://osprey.bco-dmo.org/project/896812
Collaborative Research: Pressure effects on microbially-catalyzed organic matter degradation in the deep ocean
<p><em>NSF Award Abstract:</em><br />
Microbes are important players in the carbon cycle in the ocean. These organisms consume organic carbon and produce carbon dioxide in marine systems. Because the average depth of the ocean is 4000 m, microbes must work at high pressures typical of the deep ocean (>1000 m). Although high pressure is known to affect marine microbes, their carbon cycling activities have mostly been measured at surface ocean pressures. As a result, it remains unknown how closely these measurements reflect the activities of deep-sea microbes at high pressures. As a result of collaborations with scientists in Denmark and Germany, this project will be able to use special equipment to investigate the effects of high pressures on marine microbes and their carbon cycling activities. This work is necessary to quantify rates of carbon cycling and identify the microbes involved, especially in deep waters. The project will provide training for diverse undergraduate and graduate students, and a postdoc who will conduct novel research in the U.S., Denmark, and Germany, both at sea and in the lab. The scientists will also teach middle school students about the role of microbes in the carbon cycle and pressure effects on life in the ocean. The project will provide internships for high school students, focusing on first-generation students who would like to go to college. This work may aid in future efforts to identify enzymes that function well under high pressure.</p>
<p>Heterotrophic microbes (e.g., bacteria and archaea) are found throughout the ocean. Their biogeochemical functions help determine the rates and locations at which carbon and nutrients are regenerated, as well as the extent to which organic matter is preserved. Although research has shown that pressure profoundly affects the activities of marine microbes, most investigations of microbial communities of the deep sea are conducted at atmospheric pressure, due to the limited availability of specialized equipment. In collaboration with the Danish Center for Hadal Research at the University of Southern Denmark, this study will identify the effects of pressure on microbial communities and their extracellular enzymes of pressures characteristic of bathy- and abyssopelagic depths. At sea and in the lab, the scientific team will compare the effects of depressurization on the activities of enzymes produced by microbial communities of the deep ocean, as well as the effects of high pressure on surface-water derived enzymes and communities. Fieldwork will take place in Danish coastal waters, well as in the open North Atlantic and Pacific Oceans. Using pressurization systems and in situ incubations, this study will measure hydrolysis rates of peptides and polysaccharides, two of the major classes of marine organic matter. Project activities will also focus on developing the means to measure enzyme activities in situ in the deep ocean. In collaboration with colleagues from the Max Planck Institute for Marine Microbiology in Germany, this proect will additionally investigate whether pressure affects the selfish uptake of polysaccharides. These studies will provide new insight into understudied but key factors that help determine the fate of organic matter in the deep ocean.</p>
<p>This project is funded by the Biological and Chemical Oceanography Programs.</p>
<p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p>
Pressure effects on microbes
largerWorkCitation
project
eng; USA
biota
oceans
-73.03333
-60.0479
34.98703
42.17828
2024-05-10
2024-05-19
Western North Atlantic, hadal depths of the Pacific
0
BCO-DMO catalogue of parameters from Bacterial productivity of samples from three stations in the Western North Atlantic aboard R/V Atlantic Explorer cruise AE2413 during May 2024
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/963762.rdf
Name: deployment
Units: unitless
Description: <p>Cruise ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/963763.rdf
Name: station
Units: unitless
Description: <p>Station number 24, 25, 26.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963764.rdf
Name: latitude_n
Units: Decimal degrees
Description: <p>Latitude of sampling site, south is negative.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963765.rdf
Name: longitude_e
Units: Decimal degrees
Description: <p>Longitude of sampling site, west is negative.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963766.rdf
Name: ISO_DateTime_UTC
Units: unitless
Description: <p>Datetime of collection in ISO format, UTC.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963767.rdf
Name: date
Units: unitless
Description: <p>Date of sample collection.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963768.rdf
Name: time_local_est
Units: unitless
Description: <p>Time of sample collection (local time), US Eastern Time (UTC-05:00)</p>
http://lod.bco-dmo.org/id/dataset-parameter/963769.rdf
Name: cast_number
Units: unitless
Description: <p>Cast number (refers to cast of CTD/Niskin bottles on cruise)</p>
http://lod.bco-dmo.org/id/dataset-parameter/963770.rdf
Name: depth_description
Units: unitless
Description: <p>Water column feature or oceanic zone sampled DCM (Deep Chlorophyll Maximum), OMZ (Oxygen Minimum Zone), Bathy, or Deep (bottom or near bottom). Station 26 DCM was not measured due to sampling error.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963771.rdf
Name: depth_actual
Units: m
Description: <p>Actual depth at which water was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/963772.rdf
Name: insitu_temp
Units: degrees Celsius
Description: <p>Temperature of the samples in-situ.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963773.rdf
Name: sample_type
Units: unitless
Description: <p>The type of sample, whether it was incubated using water from the bulk water column, sediments, or amended</p>
http://lod.bco-dmo.org/id/dataset-parameter/963774.rdf
Name: incubation_type
Units: unitless
Description: <p>The type of incubation (in epitube or excitaner vial at atmospheric pressure or in excitaner vial in pressure vessel)</p>
http://lod.bco-dmo.org/id/dataset-parameter/963775.rdf
Name: incubation_pressure
Units: MPa
Description: <p>Amount of pressure applied during incubation</p>
http://lod.bco-dmo.org/id/dataset-parameter/963776.rdf
Name: incubation_temp
Units: degrees Celsius
Description: <p>Temperature of 3H-Leucine incubation.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963777.rdf
Name: unamended_amended
Units: unitless
Description: <p>Whether the sample was amended (A) or unamended (U).</p>
http://lod.bco-dmo.org/id/dataset-parameter/963778.rdf
Name: substrate
Units: unitless
Description: <p>3H-leucine</p>
http://lod.bco-dmo.org/id/dataset-parameter/963779.rdf
Name: incubation_time
Units: hours
Description: <p>Amount of time in hours samples were incubated with 3H-leu prior to addition of TCA</p>
http://lod.bco-dmo.org/id/dataset-parameter/963780.rdf
Name: DPM_Kill
Units: disintegrations per minute (dpm)
Description: <p>Radioactivity of incorporated 3H-leucine in disintegrations per minute of killed control.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963781.rdf
Name: DPM_rep1
Units: disintegrations per minute (dpm)
Description: <p>Radioactivity of incorporated 3H-leucine in disintegrations per minute of replicate 1.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963782.rdf
Name: DPM_rep2
Units: disintegrations per minute (dpm)
Description: <p>Radioactivity of incorporated 3H-leucine in disintegrations per minute of replicate 2.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963783.rdf
Name: DPM_rep3
Units: disintegrations per minute (dpm)
Description: <p>Radioactivity of incorporated 3H-leucine in disintegrations per minute of replicate 3.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963784.rdf
Name: Average_incorp
Units: pmol L-1
Description: <p>Amount of incorporated 3H-leucine in picomoles per liter (average radioactivity of replicates in excess of radioactivity of killed control relative to the radioactivity of a standard amount of 3H-Leucine).</p>
http://lod.bco-dmo.org/id/dataset-parameter/963785.rdf
Name: H3_Leu
Units: pmol L-1 h-1
Description: <p>Amount of incorporated 3H-leucine in picomoles per liter per hour.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963786.rdf
Name: stdev
Units: pmol L-1 h-1
Description: <p>Standard deviation in the amount of incorporated 3H-leucine in picomoles per liter per hour.</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
4717
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/dca33499-b946-40b7-8979-b143ee4eeb9b/content
download
https://doi.org/10.26008/1912/bco-dmo.963407.1
download
onLine
dataset
<p>Water for incubation &nbsp;was collected via Niskin bottles mounted on a rosette, equipped with a CTD. &nbsp;Bulk water was collected into an acid washed 50 mL Falcon tube directly from niskin bottles.&nbsp;</p>
<p>Isotopically diluted&nbsp;L-[3,4,5-3H(N)]-Leucine (Revvity, NET460250UC,&nbsp;specific activity of&nbsp;3.811 TBq/mmol) was added to 1.7ml triplicate subsamples and one TCA killed control&nbsp;(20 nM final concentration). &nbsp;Samples and killed control were&nbsp;incubated between 5 and 48 hours at nearly in-situ temperature or 4°C.&nbsp; Following incubation, live samples were killed with 100% (w/v) TCA and all samples were centrifuged (10,000 rpm at 4°C for 10 min) to pelletize cell material.&nbsp; The supernatant liquid was removed and 1 mL of ice cold 5% (w/v) TCA solution was added, followed by vortex mixing and centrifugation.&nbsp; Supernatant removal, mixing, and centrifugation were repeated using 1 mL of ice cold 80% ethanol solution.&nbsp; Again, the supernatant liquid was removed and each sample was left to dry in a hood overnight.&nbsp; After drying, 1 mL of scintillation cocktail (ScintiSafe 30% Cocktail, Fisher SX23-5) was added and left overnight&nbsp;so that&nbsp;precipitated proteins dissolve into scintillation fluid.&nbsp; Incorporated radioactivity was measured using a PerkinElmer Tri-Carb 2910TR LSA scintillation counter.&nbsp; Radioactivity was compared to 1 mL of scintillation cocktail spiked with an identical amount of&nbsp;isotopically diluted&nbsp;L-[3,4,5-3H(N)]-Leucine that was added to samples. &nbsp;Incorporation rate was calculated by dividing sample radioactivity by incubation time.</p>
Specified by the Principal Investigator(s)
<p>Data were processed using Microsoft Excel.</p>
Specified by the Principal Investigator(s)
- Imported "20250424_BCODMO_AE2413 Bulk water_3H-Leucine_incorporation_csv.csv" into BCO-DMO system
- Removed two rows where time is NULL at submitter's request
- Converted "date" to YYYY-MM-DD format
- Created new ISO formatted datetime in UTC
- Removed string "MPa" from the "incubation_pressure" values
- Renamed fields to remove spaces and units from parameters to comply with BCO-DMO system and style requirements
- Exported file as "963407_v1_bacterial_productivity.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
CTD
CTD
PI Supplied Instrument Name: CTD PI Supplied Instrument Description:Water for incubation was collected via Niskin bottles mounted on a rosette, equipped with a CTD. Bulk water was collected into an acid washed 50 mL Falcon tube directly from niskin bottles. Instrument Name: CTD - profiler Instrument Short Name: Instrument Description: The Conductivity, Temperature, Depth (CTD) unit is an integrated instrument package designed to measure the conductivity, temperature, and pressure (depth) of the water column. The instrument is lowered via cable through the water column. It permits scientists to observe the physical properties in real-time via a conducting cable, which is typically connected to a CTD to a deck unit and computer on a ship. The CTD is often configured with additional optional sensors including fluorometers, transmissometers and/or radiometers. It is often combined with a Rosette of water sampling bottles (e.g. Niskin, GO-FLO) for collecting discrete water samples during the cast.
This term applies to profiling CTDs. For fixed CTDs, see https://www.bco-dmo.org/instrument/869934. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/130/
PerkinElmer Tri-Carb 2910TR LSA scintillation counter
PerkinElmer Tri-Carb 2910TR LSA scintillation counter
PI Supplied Instrument Name: PerkinElmer Tri-Carb 2910TR LSA scintillation counter PI Supplied Instrument Description:Incorporated radioactivity was measured using a PerkinElmer Tri-Carb 2910TR LSA scintillation counter. Instrument Name: Liquid Scintillation Counter Instrument Short Name:LSC Instrument Description: Liquid scintillation counting is an analytical technique which is defined by the incorporation of the radiolabeled analyte into uniform distribution with a liquid chemical medium capable of converting the kinetic energy of nuclear emissions into light energy. Although the liquid scintillation counter is a sophisticated laboratory counting system used to quantify the activity of particulate emitting (ß and a) radioactive samples, it can also detect the auger electrons emitted from 51Cr and 125I samples.
Liquid scintillation counters are instruments assaying alpha and beta radiation by quantitative detection of visible light produced by the passage of rays or particles through a suitable scintillant incorporated into the sample. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB21/
Niskin bottles
Niskin bottles
PI Supplied Instrument Name: Niskin bottles PI Supplied Instrument Description:Water for incubation was collected via Niskin bottles mounted on a rosette, equipped with a CTD. Bulk water was collected into an acid washed 50 mL Falcon tube directly from niskin bottles. 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/
Cruise: AE2413
AE2413
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel
AE2413
John Paul Balmonte
University of Southern Denmark
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel