http://lod.bco-dmo.org/id/dataset/717503
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
2017-10-24
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Bacterial protein production on particles obtained by gravity filtration of water collected on RV/Endeavor EN556 (Patterns of activities project)
2017-10-27
publication
2017-10-27
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2020-05-13
publication
https://doi.org/10.26008/1912/bco-dmo.717503.1
Carol Arnosti
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: Arnosti, C. (2020) Bacterial protein production on particles obtained by gravity filtration of water collected on RV/Endeavor EN556 (Patterns of activities project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2017-10-27 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.717503.1 [access date]
Bacterial protein production from gravity filtered seawater, EN556 Dataset Description: <p>Experiments on (operationally defined) particles were carried out by gravity-filtering water through 3 um pore size filters. Bacterial protein production was measured from <sup>3</sup>H-leucine incorporation by heterotrophic bacteria.</p>
<p>See Niskin Bottle and Cast List EN556 to link specific casts and bottles to each experiment: <a href="https://www.bco-dmo.org/dataset/717427" target="_blank">https://www.bco-dmo.org/dataset/717427</a>.</p> Methods and Sampling: <p>Seawater was transferred to 20 L carboys that were rinsed three times with water from the sampling depth. Experiments on (operationally defined) particles were carried out by gravity-filtering water through 3 um pore size filters.&nbsp;Fractions of the filters (1/8 of each filter) was incubated in autoclaved seawater from the same depth/station; bacterial protein production was calculated to account for the volume of seawater that had passed through the filter.</p>
<p>Bacterial protein production was measured from 3H-leucine incorporation by heterotrophic bacteria using the cold trichloroacetic acid (TCA) and microcentrifuge extraction method [as in Kirchman, 2001]. All work was performed aboard ship. In brief, triplicate live samples of 1.5 mL seawater as well as one 100% (w/v) TCA-killed control were incubated with 23 uL of L-[3,4,5-3H(N)]-Leucine (PerkinElmer, NET460250UC) for between 4 and 24 hours in the dark at as close to in situ temperature as possible. Live samples were then killed with 89 uL of 100% (w/v) TCA and centrifuged (10,000 rpm at 4°C for 10 min) to pelletize cell material.&nbsp; The supernatant liquid was removed and 1 mL of 5% (w/v) TCA solution was added, followed by vortex mixing and centrifugation. Supernatant removal, mixing, and centrifugation were repeated using 1 mL of 80% ethanol solution.&nbsp; Finally, the supernatant liquid was removed and each sample was dried overnight.&nbsp; After drying, 1 mL of scintillation cocktail (ScintiSafe 30% Cocktail, Fisher SX23-5) was added and incorporated radioactivity was measured using an LSA scintillation counter (PerkinElmer Tri-Carb 2910TR). Leucine incorporation rate was calculated from the incorporated radioactivity, compared to 1 mL of scintillation cocktail spiked with 23 uL of L-[3,4,5-3H(N)]-Leucine radioactivity, divided by incubation time.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1332881 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1332881
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
asNeeded
Dataset Version: 1
Unknown
cruise_id
cast
station
depth_id
depth_m
lat_degdecmin
lon_degdecmin_W
lat_dec
lon_dec
temp
salinity
timepoint
time_elapsed_hr
Leu_3H_rep_1
Leu_3H_rep_2
Leu_3H_rep_3
LSA scintillation counter, PerkinElmer Tri-Carb 2910TR
20 liter Niskin bottles
theme
None, User defined
Cruise identfier
cast
station
depth_comment
depth
latitude
longitude
water temperature at measurement depth
salinity
time_point
time_elapsed
leucine incorporation rate
featureType
BCO-DMO Standard Parameters
Centrifuge
Liquid Scintillation Counter
Niskin bottle
Shipboard Incubator
instrument
BCO-DMO Standard Instruments
EN556
service
Deployment Activity
North Atlantic, shelf waters off Rhode Island, then a transect along Line W (farthest stn: ca 37 N, 68W, approximately at ID #9020)
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.
Latitudinal and depth-related contrasts in enzymatic capabilities of pelagic microbial communities: Predictable patterns in the ocean?
https://osprey.bco-dmo.org/project/712359
Latitudinal and depth-related contrasts in enzymatic capabilities of pelagic microbial communities: Predictable patterns in the ocean?
<p><em>NSF Award Abstract:</em><br />
Heterotrophic microbial communities are key players in the marine carbon cycle, transforming and respiring organic carbon, regenerating nutrients, and acting as the final filter in sediments through which organic matter passes before long-term burial. Microbially-driven carbon cycling in the ocean profoundly affects the global carbon cycle, but key factors determining rates and locations of organic matter remineralization are unclear. In this study, researchers from the University of North Carolina at Chapel Hill will investigate the ability of pelagic microbial communities to initiate the remineralization of polysaccharides and proteins, which together constitute a major pool of organic matter in the ocean. Results from this study will be predictive on a large scale regarding the nature of the microbial response to organic matter input, and will provide a mechanistic framework for interpreting organic matter reactivity in the ocean.</p>
<p>Broader Impacts: This study will provide scientific training for undergraduate and graduate students from underrepresented groups. The project will also involve German colleagues, thus strengthening international scientific collaboration.</p>
Patterns of activities
largerWorkCitation
project
eng; USA
biota
oceans
North Atlantic, shelf waters off Rhode Island, then a transect along Line W (farthest stn: ca 37 N, 68W, approximately at ID #9020)
-71.0052
-68.4037
37.6041
40.0702
2015-04-27
2015-05-02
Atlantic Ocean, Arctic Ocean, Pacific Ocean, Greenland
0
BCO-DMO catalogue of parameters from Bacterial protein production on particles obtained by gravity filtration of water collected on RV/Endeavor EN556 (Patterns of activities 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/718031.rdf
Name: cruise_id
Units: unitless
Description: <p>cruise identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/718032.rdf
Name: cast
Units: unitless
Description: <p>cast number</p>
http://lod.bco-dmo.org/id/dataset-parameter/718033.rdf
Name: station
Units: unitless
Description: <p>station number</p>
http://lod.bco-dmo.org/id/dataset-parameter/718034.rdf
Name: depth_id
Units: unitless
Description: <p>depth description: sequence of depths sampled with 1 is surface and higher numbers at greater depths</p>
http://lod.bco-dmo.org/id/dataset-parameter/718035.rdf
Name: depth_m
Units: meters
Description: <p>actual depth at which water collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/718036.rdf
Name: lat_degdecmin
Units: degrees and decimal minutes
Description: <p>latitude formatted as degrees.decimal_minutes</p>
http://lod.bco-dmo.org/id/dataset-parameter/718037.rdf
Name: lon_degdecmin_W
Units: degrees and decimal minutes
Description: <p>longitude formatted as degrees.decimal_minutes</p>
http://lod.bco-dmo.org/id/dataset-parameter/718038.rdf
Name: lat_dec
Units: decimal degrees
Description: <p>latitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/718039.rdf
Name: lon_dec
Units: decimal degrees
Description: <p>longitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/718040.rdf
Name: temp
Units: degrees Celsius
Description: <p>water temperature as determined by CTD</p>
http://lod.bco-dmo.org/id/dataset-parameter/718041.rdf
Name: salinity
Units: per mil
Description: <p>salinity as determined by CTD</p>
http://lod.bco-dmo.org/id/dataset-parameter/718042.rdf
Name: timepoint
Units: unitless
Description: <p>sampling time point (0; 1; 2; etc.) post-incubation</p>
http://lod.bco-dmo.org/id/dataset-parameter/718043.rdf
Name: time_elapsed_hr
Units: hours
Description: <p>hours elapsed to reach a specific timepoint</p>
http://lod.bco-dmo.org/id/dataset-parameter/718044.rdf
Name: Leu_3H_rep_1
Units: picomol leucine/liter/hour
Description: <p>replicate 1 of leucine incorporation rate (bacterial protein production)</p>
http://lod.bco-dmo.org/id/dataset-parameter/718045.rdf
Name: Leu_3H_rep_2
Units: picomol leucine/liter/hour
Description: <p>replicate 2 of leucine incorporation rate (bacterial protein production)</p>
http://lod.bco-dmo.org/id/dataset-parameter/718046.rdf
Name: Leu_3H_rep_3
Units: picomol leucine/liter/hour
Description: <p>replicate 3 of leucine incorporation rate (bacterial protein production)</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
917
https://darchive.mblwhoilibrary.org/bitstream/1912/25771/1/dataset-717503_en556-gravity-filtered-particle-associated-bacterial-production__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.717503.1
download
onLine
dataset
<p>Seawater was transferred to 20 L carboys that were rinsed three times with water from the sampling depth. Experiments on (operationally defined) particles were carried out by gravity-filtering water through 3 um pore size filters.&nbsp;Fractions of the filters (1/8 of each filter) was incubated in autoclaved seawater from the same depth/station; bacterial protein production was calculated to account for the volume of seawater that had passed through the filter.</p>
<p>Bacterial protein production was measured from 3H-leucine incorporation by heterotrophic bacteria using the cold trichloroacetic acid (TCA) and microcentrifuge extraction method [as in Kirchman, 2001]. All work was performed aboard ship. In brief, triplicate live samples of 1.5 mL seawater as well as one 100% (w/v) TCA-killed control were incubated with 23 uL of L-[3,4,5-3H(N)]-Leucine (PerkinElmer, NET460250UC) for between 4 and 24 hours in the dark at as close to in situ temperature as possible. Live samples were then killed with 89 uL of 100% (w/v) TCA and centrifuged (10,000 rpm at 4°C for 10 min) to pelletize cell material.&nbsp; The supernatant liquid was removed and 1 mL of 5% (w/v) TCA solution was added, followed by vortex mixing and centrifugation. Supernatant removal, mixing, and centrifugation were repeated using 1 mL of 80% ethanol solution.&nbsp; Finally, the supernatant liquid was removed and each sample was dried overnight.&nbsp; After drying, 1 mL of scintillation cocktail (ScintiSafe 30% Cocktail, Fisher SX23-5) was added and incorporated radioactivity was measured using an LSA scintillation counter (PerkinElmer Tri-Carb 2910TR). Leucine incorporation rate was calculated from the incorporated radioactivity, compared to 1 mL of scintillation cocktail spiked with 23 uL of L-[3,4,5-3H(N)]-Leucine radioactivity, divided by incubation time.</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing Notes:</strong><br />
- added conventional header with dataset name, PI name, version date<br />
- modified parameter names to conform with BCO-DMO naming conventions<br />
- converted lat and lon to decimal degrees<br />
- added cruise_id column<br />
- replaced 'NA' and blank cells with 'nd' (no data)<br />
-&nbsp;removed from display the following columns with no data: NO2_NO3_uM, NH4_uM, PO4_uM, DOC_uM, cells_per_mL</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
PI Supplied Instrument Name: PI Supplied Instrument Description:Used to concentrate cell material. Instrument Name: Centrifuge Instrument Short Name: Instrument Description: A machine with a rapidly rotating container that applies centrifugal force to its contents, typically to separate fluids of different densities (e.g., cream from milk) or liquids from solids.
LSA scintillation counter, PerkinElmer Tri-Carb 2910TR
LSA scintillation counter, PerkinElmer Tri-Carb 2910TR
PI Supplied Instrument Name: LSA scintillation counter, PerkinElmer Tri-Carb 2910TR PI Supplied Instrument Description:Used to measure incorporated radioactive 3H-leucine 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/
20 liter Niskin bottles
20 liter Niskin bottles
PI Supplied Instrument Name: 20 liter Niskin bottles PI Supplied Instrument Description:Used to collect water for large volume mesocosm experiments 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/
PI Supplied Instrument Name: Instrument Name: Shipboard Incubator Instrument Short Name: Instrument Description: A device mounted on a ship that holds water samples under conditions of controlled temperature or controlled temperature and illumination.
Cruise: EN556
EN556
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel
EN556
Carol Arnosti
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel