http://lod.bco-dmo.org/id/dataset/877100
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
2022-07-18
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Processed CTD data with thermodynamic calculations from R/V Atlantic Explorer cruise AE2207 to the Bermuda Atlantic Time Series (BATS) station in April 2022
2022-07-21
publication
2022-07-21
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2022-07-21
publication
https://doi.org/10.26008/1912/bco-dmo.877100.1
Steven W. Wilhelm
University of Tennessee Knoxville
principalInvestigator
Matthew Sullivan
Ohio State University
principalInvestigator
Joshua Weitz
Georgia 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: Muratore, D., Wilhelm, S. W., Sullivan, M., Weitz, J. (2022) Processed CTD data with thermodynamic calculations from R/V Atlantic Explorer cruise AE2207 to the Bermuda Atlantic Time Series (BATS) station in April 2022. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2022-07-21 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.877100.1 [access date]
AE2207 Processed CTD with Thermodynamic Calculations Dataset Description: Methods and Sampling: <p>CTD packages with Niskin rosettes were deployed to 300 meters with the exception of two deep casts: C01 to 2000 meters (where PAR sensor was removed) and C13 to 1000 meters. All deployments began with a 4-5 minute soak at 15m to initialize the pumps and stabilize instrument readings. Casts are identified by two-digit ids preceded by a C, so that C01 is the first cast and C10 is the tenth cast etc.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1829636 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1829636
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1829640 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1829640
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1829641 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1829641
completed
Steven W. Wilhelm
University of Tennessee Knoxville
865-974-0665
1499 Circle Dr Room 637
Knoxville
TN
37996
USA
wilhelm@utk.edu
pointOfContact
Matthew Sullivan
Ohio State University
614-247-1616
496 W 12th Ave Riffe Building
Columbus
OH
43210
USA
sullivan.948@osu.edu
pointOfContact
Joshua Weitz
Georgia Institute of Technology
404-894-3700
310 Ferst Dr.
Atlanta
GA
30332
USA
jsweitz@gatech.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
cast
ISO_DateTime_UTC
lat
lon
pressure
corrected_depth
par_value
par_relative
temp
absolute_salinity
density
fluor
beam
oxygen
oxy_sol
oxy_sat
mld
dcm
Altimeter (Valeport) - VA500
Licor PAR sensor (Biospherical Instruments) QSP-2300
CTD unit (Seabird) SBE 9+
Fluorometer (Wet Labs) ECO-FLRTD
Fluorometer (Chelsea) Aquatracka
Oxygen sensors (Seabird) SBE 43
Conductivity sensor (Seabird) SBE 4C
Transmissometer (Wet Labs) C-Star
Temperature profiler (Seabird) SBE 3F (and 3+ secondary unit)
Reversing Thermometer (Seabird) SBE 35RT
theme
None, User defined
cast
ISO_DateTime_UTC
latitude
longitude
water pressure
depth
PAR
water temperature at measurement depth
salinity
sigma-theta
fluorescence
beam attenuation
dissolved Oxygen
O2 saturation
mixed layer depth
featureType
BCO-DMO Standard Parameters
Altimeter
Biospherical PAR sensor
CTD Sea-Bird
CTD-fluorometer
CTD-fluorometer
Sea-Bird SBE 43 Dissolved Oxygen Sensor
Sea-Bird SBE-4 Conductivity Sensor
Transmissometer
Water Temperature Sensor
Water Temperature Sensor
instrument
BCO-DMO Standard Instruments
AE2207
service
Deployment Activity
Bermuda Atlantic Time Series station
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: Inferring Cellular Lysis and Regeneration of Organic Matter by Marine Viruses
https://osprey.bco-dmo.org/project/775816
Collaborative Research: Inferring Cellular Lysis and Regeneration of Organic Matter by Marine Viruses
<p><em>NSF Award Abstract:</em><br />
Viral infections of marine microbes can transform the fate of microbial populations that fuel global ocean biogeochemical cycles. For example, viral infections of microbes lead to the release of carbon and nutrients back into the environment. This regeneration of carbon and nutrients stimulates the activity of other microbes and diverts carbon and nutrients from larger organisms in marine food webs. Because virus-microbe infections are relatively specific, it is critical to identify those pairs of viruses and microbes that may disproportionally contribute to the turnover of carbon and nutrients in the ocean. This project will develop quantitative approaches and tools to quantify which viruses infect which microbes and to use these data to quantify how viral infections of microbes collectively shape nutrient and carbon cycles in the North Atlantic Ocean. The project will analyze virus-microbe interactions in mesocosms at the Bigelow Laboratory for Ocean Sciences in mid-coast Maine and during open ocean expeditions to the Bermuda Atlantic Time-Series Study (BATS) site. An interdisciplinary team will leverage recent advances in molecular biology, computational biology, and mathematical modeling to identify virus-host partners and their impact on the movement of elements through marine systems. This project will support three graduate students, six undergraduate students and one postdoctoral researcher in an interdisciplinary context. Research advances will be translated into reproducible software methods to be disseminated via the community cyberinfrastructure platform iVirus, with additional training materials presented as part of a viral methods and informatics workshop held at The Ohio State University. The translation of discoveries to the public will be furthered by the involvement of journalism undergraduate students at the University of Tennessee-Knoxville.</p>
<p>This project builds upon advances in the molecular toolkit of viromics to develop an integrated approach to characterize lineage-specific rates of infection, lysis, and nutrient release induced by marine viruses in open ocean ecosystems. It will combine theory, in vitro experiments, and in situ sampling to (i) extend a robust inference method for estimating virus-microbe cross-infection networks from time-series data; (ii) establish and characterize in-vitro protocols for inferring cross-infectivity in complex communities using culture-independent methods; (iii) estimate lineage-specific rates of lysis and regeneration of nutrients in marine systems, including applications to coastal and open ocean ecosystems. Project aims focus on quantifying the extent to which virus-induced lysis and regeneration of carbon and nutrients is heterogeneously distributed across microbial populations. To do so, the project will incorporate time series measurements of abundance information (via metagenomes) and activity information (via metatranscriptomes). In so doing, it will advance efforts to understand community-scale interactions rather than those amongst a single virus-host pair. Theoretical methods and in vitro protocols will directly infer lineage-specific infection, lysis, and nutrient release rates in coastal- and open-ocean ecosystems in the North Atlantic Ocean. Results will be used to identify key links that disproportionately influence bulk nutrient release. A novel PCR-based approach will augment and validate the core inference approach. Overall, the project aims to enhance our understanding of how viruses contribute to marine ecosystem function.</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>
InVirT
largerWorkCitation
project
eng; USA
oceans
Bermuda Atlantic Time Series station
-64.59317
-64.16483
31.0265
31.66367
2022-04-22
2022-04-25
Bermuda Atlantic Time Series
0
BCO-DMO catalogue of parameters from Processed CTD data with thermodynamic calculations from R/V Atlantic Explorer cruise AE2207 to the Bermuda Atlantic Time Series (BATS) station in April 2022
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/877122.rdf
Name: cast
Units: unitless
Description: <p>Identifier for individual cast</p>
http://lod.bco-dmo.org/id/dataset-parameter/877123.rdf
Name: ISO_DateTime_UTC
Units: unitless
Description: <p>CTD deployment date and time in UTC; format is ISO8601: YYYY-MM-DDThh:mm:ssZ</p>
http://lod.bco-dmo.org/id/dataset-parameter/877124.rdf
Name: lat
Units: degrees North
Description: <p>Latitude at time of deployment</p>
http://lod.bco-dmo.org/id/dataset-parameter/877125.rdf
Name: lon
Units: degrees East
Description: <p>Longitude at time of deployment</p>
http://lod.bco-dmo.org/id/dataset-parameter/877126.rdf
Name: pressure
Units: decibars (dbar)
Description: <p>Pressure</p>
http://lod.bco-dmo.org/id/dataset-parameter/877127.rdf
Name: corrected_depth
Units: meters (m)
Description: <p>Height relative to sea surface</p>
http://lod.bco-dmo.org/id/dataset-parameter/877128.rdf
Name: par_value
Units: microEinsteins per squre centimeter per second (uE/cm^2s)
Description: <p>PAR</p>
http://lod.bco-dmo.org/id/dataset-parameter/877129.rdf
Name: par_relative
Units: percent (%)
Description: <p>Corrected irradiance (same as cpar in 'Unprocessed' CTD dataset)</p>
http://lod.bco-dmo.org/id/dataset-parameter/877130.rdf
Name: temp
Units: degrees Celsius
Description: <p>Temperature</p>
http://lod.bco-dmo.org/id/dataset-parameter/877131.rdf
Name: absolute_salinity
Units: grams per kilogram (g/kg)
Description: <p>Derived absolute salinity</p>
http://lod.bco-dmo.org/id/dataset-parameter/877132.rdf
Name: density
Units: kilograms per cubic meter (kg/m^3)
Description: <p>Derived sigma-theta from reference depth of 0</p>
http://lod.bco-dmo.org/id/dataset-parameter/877133.rdf
Name: fluor
Units: milligrams per cubic meter (mg/m^3)
Description: <p>Wet Labs ECO Chlorophyll Fluorescence</p>
http://lod.bco-dmo.org/id/dataset-parameter/877134.rdf
Name: beam
Units: reciprocal meters (1/m)
Description: <p>Wet Labs C-Star Beam Attenuation</p>
http://lod.bco-dmo.org/id/dataset-parameter/877135.rdf
Name: oxygen
Units: micromoles per kilogram (umol/kg)
Description: <p>Oxygen concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/877136.rdf
Name: oxy_sol
Units: micromoles per kilogram (umol/kg)
Description: <p>Derived oxygen solubility</p>
http://lod.bco-dmo.org/id/dataset-parameter/877137.rdf
Name: oxy_sat
Units: percent (%)
Description: <p>Derived oxygen saturation</p>
http://lod.bco-dmo.org/id/dataset-parameter/877138.rdf
Name: mld
Units: meters (m)
Description: <p>Mixed layer depth using a change in sigma-theta from 10dbar of 0.125</p>
http://lod.bco-dmo.org/id/dataset-parameter/877139.rdf
Name: dcm
Units: meters (m)
Description: <p>Deep chlorophyll maximum depth</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
2547942
https://darchive.mblwhoilibrary.org/bitstream/1912/29152/1/dataset-877100_ae2207-processed-ctd-thermodynamic-calculations__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.877100.1
download
onLine
dataset
<p>CTD packages with Niskin rosettes were deployed to 300 meters with the exception of two deep casts: C01 to 2000 meters (where PAR sensor was removed) and C13 to 1000 meters. All deployments began with a 4-5 minute soak at 15m to initialize the pumps and stabilize instrument readings. Casts are identified by two-digit ids preceded by a C, so that C01 is the first cast and C10 is the tenth cast etc.</p>
Specified by the Principal Investigator(s)
<p><strong>Data Processing:</strong><br />
Data were converted from .hex files to .cnv files using SeaSave on default parameters. Then, each file was read using the seabird python library (<a href="https://github.com/castelao/seabird" target="_blank">https://github.com/castelao/seabird</a>), and cast latitude, longitude, and deployment time were retrieved. For further calculations, pressure, temperature (primary sensor), conductivity (primary sensor), oxygen (primary sensor), beam attenuation, ECO chlorophyll fluorescence, PAR, corrected PAR, and instrument time were retained. Due to a choppy sea state, data from the upper 5 db were trimmed as the measurements were noisy. Then, all scans from the first 4.5 minutes of the cast were removed as these data were associated with the initializing soak at 15m before profiling. Finally, the upcast was removed to retain the downcast.</p>
<p>Using the python implementation of the Gibbs SeaWater oceanographic toolbox from TEOS-10 (<a href="https://www.teos-10.org/pubs/gsw/html/gsw_front_page.html" target="_blank">https://www.teos-10.org/pubs/gsw/html/gsw_front_page.html</a>), the following thermodynamic calculations were conducted. A corrected depth (height relative to sea surface, meaning a negative number) was calculated from the pressure and latitude. Then, potential salinity was calculated using conductivity, temperature, and pressure. Absolute salinity was calculated from potential salinity, and conservative temperature was calculated from absolute salinity, temperature, and pressure. Density in terms of sigma-theta was calculated using absolute salinity and conservative temperature. Then, oxygen solubility was calculated using the GSW oxygen solubility function with absolute salinity, conservative temperature, pressure, latitude, and longitude. Oxygen saturation was estimated for each scan using the primary oxygen sensor and the derived oxygen solubility. The outputs for the transformed data for each retained scan are contained in the file [first file]. Then, to remove additional instrument noise and standardize profiles across casts, data were smoothed and interpolated to every 0.5 dbar of pressure with a Nadaraya-Watson kernel estimator using a bandwidth of 5 meters. Using the smoothed and binned outputs, the mixed layer depth was calculated using the criterion of an increase in sigma-theta above 0.125 from 10dbar. Then, the DCM depth was calculated by identifying the depth corresponding to the highest chlorophyll fluorescence below the mixed layer depth. The derived mixed layer and dcm depths, as well as the smoothed and 0.5 dbar binned values for the above mentioned variables are included in the file [file 2].</p>
<p><strong>BCO-DMO Processing:</strong><br />
- replaced "NA" with "nd" to indicate "no data";<br />
- converted date/time field to ISO8601 format;<br />
- removed the "id" field (identical to "cast").</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
Altimeter (Valeport) - VA500
Altimeter (Valeport) - VA500
PI Supplied Instrument Name: Altimeter (Valeport) - VA500 Instrument Name: Altimeter Instrument Short Name:Altimeter Instrument Description: An instrument that measures height above a fixed surface. The data can be used to map ocean-surface topography and generate gridded surface height fields. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/379/
Licor PAR sensor (Biospherical Instruments) QSP-2300
Licor PAR sensor (Biospherical Instruments) QSP-2300
PI Supplied Instrument Name: Licor PAR sensor (Biospherical Instruments) QSP-2300 Instrument Name: Biospherical PAR sensor Instrument Short Name: Instrument Description: An irradiance sensor designed to measure Photosynthetically Active Radiation (PAR), manufactured by Biospherical Instruments Inc.
CTD unit (Seabird) SBE 9+
CTD unit (Seabird) SBE 9+
PI Supplied Instrument Name: CTD unit (Seabird) SBE 9+ 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/
Fluorometer (Wet Labs) ECO-FLRTD
Fluorometer (Wet Labs) ECO-FLRTD
PI Supplied Instrument Name: Fluorometer (Wet Labs) ECO-FLRTD Instrument Name: CTD-fluorometer Instrument Short Name:CTD-fluorometer Instrument Description: A CTD-fluorometer is an instrument package designed to measure hydrographic information (pressure, temperature and conductivity) and chlorophyll fluorescence. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/113/
Fluorometer (Chelsea) Aquatracka
Fluorometer (Chelsea) Aquatracka
PI Supplied Instrument Name: Fluorometer (Chelsea) Aquatracka Instrument Name: CTD-fluorometer Instrument Short Name:CTD-fluorometer Instrument Description: A CTD-fluorometer is an instrument package designed to measure hydrographic information (pressure, temperature and conductivity) and chlorophyll fluorescence. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/113/
Oxygen sensors (Seabird) SBE 43
Oxygen sensors (Seabird) SBE 43
PI Supplied Instrument Name: Oxygen sensors (Seabird) SBE 43 Instrument Name: Sea-Bird SBE 43 Dissolved Oxygen Sensor Instrument Short Name:SBE-43 DO Instrument Description: The Sea-Bird SBE 43 dissolved oxygen sensor is a redesign of the Clark polarographic membrane type of dissolved oxygen sensors. more information from Sea-Bird Electronics Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0036/
Conductivity sensor (Seabird) SBE 4C
Conductivity sensor (Seabird) SBE 4C
PI Supplied Instrument Name: Conductivity sensor (Seabird) SBE 4C Instrument Name: Sea-Bird SBE-4 Conductivity Sensor Instrument Short Name:SBE-4 Conductivity Instrument Description: The Sea-Bird SBE-4 conductivity sensor is a modular, self-contained instrument that measures conductivity from 0 to 7 Siemens/meter. The sensors (Version 2; S/N 2000 and higher) have electrically isolated power circuits and optically coupled outputs to eliminate any possibility of noise and corrosion caused by ground loops. The sensing element is a cylindrical, flow-through, borosilicate glass cell with three internal platinum electrodes. Because the outer electrodes are connected together, electric fields are confined inside the cell, making the measured resistance (and instrument calibration) independent of calibration bath size or proximity to protective cages or other objects. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0417/
Transmissometer (Wet Labs) C-Star
Transmissometer (Wet Labs) C-Star
PI Supplied Instrument Name: Transmissometer (Wet Labs) C-Star 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/
Temperature profiler (Seabird) SBE 3F (and 3+ secondary unit)
Temperature profiler (Seabird) SBE 3F (and 3+ secondary unit)
PI Supplied Instrument Name: Temperature profiler (Seabird) SBE 3F (and 3+ secondary unit) Instrument Name: Water Temperature Sensor Instrument Short Name:Water Temp Sensor Instrument Description: General term for an instrument that measures the temperature of the water with which it is in contact (thermometer). Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/134/
Reversing Thermometer (Seabird) SBE 35RT
Reversing Thermometer (Seabird) SBE 35RT
PI Supplied Instrument Name: Reversing Thermometer (Seabird) SBE 35RT Instrument Name: Water Temperature Sensor Instrument Short Name:Water Temp Sensor Instrument Description: General term for an instrument that measures the temperature of the water with which it is in contact (thermometer). Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/134/
Cruise: AE2207
AE2207
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel
AE2207
Steven W. Wilhelm
University of Tennessee Knoxville
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel