http://lod.bco-dmo.org/id/dataset/829777
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
2020-11-18
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Organismal physiological metrics from time series experiments on samples collected on R/V Atlantic Explorer cruise AE1910 in May 2019
2021-01-19
publication
2021-01-19
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-01-19
publication
https://doi.org/10.26008/1912/bco-dmo.829777.1
Amy Elizabeth Maas
Bermuda Institute of Ocean Sciences
principalInvestigator
Leocadio Blanco-Bercial
Bermuda Institute of Ocean Sciences
principalInvestigator
Ann M. Tarrant
Woods Hole Oceanographic Institution
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: Maas, A., Blanco-Bercial, L., Tarrant, A. M. (2021) Organismal physiological metrics from time series experiments on samples collected on R/V Atlantic Explorer cruise AE1910 in May 2019. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-01-19 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.829777.1 [access date]
Organismal physiological metrics from time series experiments Dataset Description: Methods and Sampling: <p>Methods detailed in Tarrant, A. M., N. McNamara-Bordewick, L. Blanco‐Bercial, A. Miccoli, and A. E. Maas. in review. Oceanic Copepods Fine-Tune Their Metabolism During Diel Vertical Migration.</p>
<p>Briefly, <em>Pleuromamma xiphias</em> were collected offshore from the Bermuda Institute of Ocean Sciences (BIOS) during a cruise aboard the R/V Atlantic Explorer from May 20-22, 2019. Net tows were conducted at 12 time points, spaced 4-7 hours apart to target mid-day, early night, mid-night and morning. Nighttime tows (early- and mid-night) were conducted using a 1-m² Reeve net deployed to 200 m depth, with 150 µm mesh size, 20 L cod end, and a miniSTAR-ODDI pressure and depth sensor. Daytime tows (morning and afternoon) were conducted using a 1-m² MOCNESS with 150 µm mesh size and a custom thermally-insulated closing cod with one closing net sampling from 400-600 m. Because the cruise coincided with Tropical Storm Andrea, it was necessary to relocate the ship twice to avoid high winds and continue sampling. The latitude, longitude, date and time (local) for each tow details this relocation. After each tow, copepods were examined under a Leica M205 C stereo microscope to identify adult P. xiphias and determine their gender. Copepods were used immediately for respirometry and excretion measurements.</p>
<p>Water for physiological experiments was obtained daily from 200 m using the rosette on the CTD. It was gravity filtered past a 0.2 µm Supor filter in a Georig 142 mm filter holder and equilibrated to 20°C in an upright incubator. At each time point, up to six copepods were transferred into individual respiration chambers that consisted of 50 mL glass syringes containing an optically sensitive oxygen sensor (OXFOIL: PyroScience, Aachen Germany) and 30 mL of 0.2 µm filtered seawater. Oxygen concentration in each chamber was then measured non-invasively and continuously (every 60 seconds) for approximately 3 hours using two FireSting optical oxygen meters (PyroScience, Aachen Germany). At the end of the experiment, the chambers were visually inspected to ensure that the copepods were still swimming. A 15-mL subsample of water was filtered at a 30º upward angle (to avoid damaging copepods or fecal pellets) through 0.7 µm GFF filters into 15-mL conical vials that had been pre-treated with OPA working reagent (21 mM sodium tetraborate, 0.063 mM sodium sulfite, 50 mL L¹ o-phthalaldehyde in ethanol). This filtered water was refrigerated (4°C) for less than 24 h and then run for ammonium measurements at sea. Ammonium was measured using the OPA (o-phthalaldehyde) method (Holmes et al. 1999). The copepod and any fecal pellets from each chamber were rinsed into a petri dish. Any fecal pellets were counted and photographed under a stereomicroscope. Copepods were rinsed once in DI water and frozen at -80ºC. Frozen copepods were subsequently weighed on a Mettler-Toledo XPR microbalance, dried, and reweighed.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1829318 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1829318
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1829378 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1829378
completed
Amy Elizabeth Maas
Bermuda Institute of Ocean Sciences
508-289-2462
17 Biological Station Ferry Reach
St.George's GE 01
Bermuda
amaas4@asu.edu
pointOfContact
Leocadio Blanco-Bercial
Bermuda Institute of Ocean Sciences
leocadio@asu.edu
pointOfContact
Ann M. Tarrant
Woods Hole Oceanographic Institution
508-289-3398
Biology Department 266 Woods Hole Rd MS #33
Woods Hole
MA
02543
USA
atarrant@whoi.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Sample_ID
net_recovery_date
net_recovery_time
lat
long
Setup_time
Gender
mL
duration
Wet_weight
Dry_weight
O2
mO2
NH4
mNH4
O_N
FP
net_recovery_ISO_DateTime_UTC
Turner fluorometer with Amonium module
1-m2 MOCNESS
FireSting optical oxygen meters
miniSTAR-ODDI
Reeve net
Mettler-Toledo XPR microbalance
theme
None, User defined
sample identification
date
time of day
latitude
longitude
sex
sample_volume
time_elapsed
weight
respiration rate
Ammonium
ratio
No BCO-DMO term
ISO_DateTime_UTC
featureType
BCO-DMO Standard Parameters
Fluorometer
MOCNESS
Niskin bottle
Oxygen Sensor
Pressure Sensor
Reeve Net
scale or balance
instrument
BCO-DMO Standard Instruments
AE1910
service
Deployment Activity
Bermuda
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: Diel physiological rhythms in a tropical oceanic copepod
https://osprey.bco-dmo.org/project/764114
Collaborative Research: Diel physiological rhythms in a tropical oceanic copepod
<p><em>NSF Award Abstract:</em><br />
The daily vertical migration (DMV) of zooplankton and fish across hundreds of meters between shallow and deep waters is a predominant pattern in pelagic ecosystems. This migration has consequences for biogeochemical cycling as it moves a substantial portion of fixed carbon and nitrogen (an estimated 15 to 40 % of the total global organic export) from the surface directly to depth where it feeds the midwater food chain and sequesters nutrients away from atmospheric mixing. Estimates and predictions of these fluxes are, however, poorly understood at present. New observations have shown that one source of uncertainty is due to the assumption that metabolic rates and processes do not vary over the course of the day, except based on changes in temperature and oxygen availability. Rates are, however, also driven by differences in feeding, swimming behavior, and underlying circadian cycles. The objective of this project is to improve the ability of scientists to understand and predict zooplankton contributions to the movement of carbon and nitrogen in the ocean by detailing daily changes in physiological processes of these organisms. By producing a set of respiration and excretion measurements over a daily time series, paired with simultaneously collected gene and protein expression patterns for an abundant vertically migratory species, the investigators will provide unprecedented and predictive insight into how changes in the environment affect the contribution of zooplankton to biogeochemical fluxes. The sampling design of the project will advance discovery and understanding by providing hands-on training opportunities to at least two undergraduate researchers. The project will broaden dissemination of the research via development of an educational module, focusing on rhythms in the ocean. The module will initially be piloted with the Bermuda Institute of Ocean Sciences (BIOS) summer camp students and then disseminated through the BIOS Explorer program, the Teacher Resources Page on the BIOS website, and published in a peer-reviewed educational journal.</p>
<p>This project will characterize the metabolic consequences of daily physiological rhythms and DVM for a model zooplankton species, the abundant subtropical copepod Pleuromamma xiphias. Flux processes (oxygen consumption, carbon dioxide production, production of ammonium and fecal pellet production) will be interrogated using directed experiments testing the effects of temperature, feeding and circadian cycle. Circadian cycling will further be examined using transcriptomic and proteomic profiling. These experiments will be related to field samples taken at 6-h intervals over the course of the diel migration using an integrated suite of molecular and organismal metrics. Combined organismal, transcriptomic and proteomic profiles will provide an understanding of which metabolic pathways and associated flux products vary in relation to particular environmental variables (food, light cycle, temperature). Diel variation in metabolic rates will also be assessed across seasons and species using other important migratory groups (pteropod, euphausiid, and another copepod). The metabolic data will then be contextualized with abundance estimates from archived depth-stratified tows to allow scaling to community-level patterns and will be used to improve calculations of zooplankton contribution to particulate organic carbon, nitrogen and respiratory active flux. The results of this study will both improve our flux estimates and provide predictive insight into how various environmental variables influence the underlying physiological pathways generating carbon and nitrogen flux.</p>
<p><strong>Cruise reports are available from the completed cruises:</strong><br />
<a href="https://www.bco-dmo.org/deployment/764871" target="_blank">SD031019</a><br />
<a href="https://www.bco-dmo.org/deployment/772516" target="_blank">AE1910</a><br />
<a href="https://www.bco-dmo.org/deployment/781440" target="_blank">AE1918</a></p>
<p><strong>Educational Resources are available for this project:</strong></p>
<p>BIOS DataBytes: <a href="https://bios.asu.edu/databytes/zooplankton-vertical-migration">Zooplankton Vertical Migration</a></p>
Zooplankton Diel Rhythm
largerWorkCitation
project
eng; USA
oceans
Bermuda
-64.7883
-64.46173
32.1311
32.5868
2019-05-20
2019-05-23
Bermuda
0
BCO-DMO catalogue of parameters from Organismal physiological metrics from time series experiments on samples collected on R/V Atlantic Explorer cruise AE1910 in May 2019
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/836582.rdf
Name: Sample_ID
Units: unitless
Description: <p>Sample ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/836583.rdf
Name: net_recovery_date
Units: unitless
Description: <p>Net recovery date; format: MM/DD/YYYY (in the local time zone, Atlantic Standard Time)</p>
http://lod.bco-dmo.org/id/dataset-parameter/836584.rdf
Name: net_recovery_time
Units: unitless
Description: <p>Net recovery time; format: hh:mm (in the local time zone, Atlantic Standard Time)</p>
http://lod.bco-dmo.org/id/dataset-parameter/836585.rdf
Name: lat
Units: degrees North
Description: <p>Latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/836586.rdf
Name: long
Units: degrees East
Description: <p>Longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/836587.rdf
Name: Setup_time
Units: unitless
Description: <p>Setup time; format: hh:mm (in the local time zone, Atlantic Standard Time)</p>
http://lod.bco-dmo.org/id/dataset-parameter/836588.rdf
Name: Gender
Units: unitless
Description: <p>Gender (M or F)</p>
http://lod.bco-dmo.org/id/dataset-parameter/836589.rdf
Name: mL
Units: milliliters (mL)
Description: <p>Sample volume</p>
http://lod.bco-dmo.org/id/dataset-parameter/836590.rdf
Name: duration
Units: hours
Description: <p>Duration</p>
http://lod.bco-dmo.org/id/dataset-parameter/836591.rdf
Name: Wet_weight
Units: milligrams (mg)
Description: <p>Wet weight</p>
http://lod.bco-dmo.org/id/dataset-parameter/836592.rdf
Name: Dry_weight
Units: milligrams (mg)
Description: <p>Dry weight</p>
http://lod.bco-dmo.org/id/dataset-parameter/836593.rdf
Name: O2
Units: micromoles O2 per hour per liter (umol O2 h-1 L-1)
Description: <p>Respiration rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/836594.rdf
Name: mO2
Units: micromoles O2 per hour per milligram (umol O2 h-1 mg-1)
Description: <p>Mass specific respiration rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/836595.rdf
Name: NH4
Units: micromoles NH4 per liter (umol NH4 L-1)
Description: <p>Ammonium excretion rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/836596.rdf
Name: mNH4
Units: micromoles NH4 per hour per milligram (umol NH4 h-1 mg-1)
Description: <p>Mass specific ammonium excretion rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/836597.rdf
Name: O_N
Units: unitless
Description: <p>O:N ratio</p>
http://lod.bco-dmo.org/id/dataset-parameter/836598.rdf
Name: FP
Units: pellets
Description: <p>Fecal Pellet production</p>
http://lod.bco-dmo.org/id/dataset-parameter/836939.rdf
Name: net_recovery_ISO_DateTime_UTC
Units: unitless
Description: <p>Net recovery date and time (UTC) in ISO8601 format: YYYY-MM-DDThh:mmZ</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
8456
https://darchive.mblwhoilibrary.org/bitstream/1912/26587/1/dataset-829777_ae1910-organismal-physiology__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.829777.1
download
onLine
dataset
<p>Methods detailed in Tarrant, A. M., N. McNamara-Bordewick, L. Blanco‐Bercial, A. Miccoli, and A. E. Maas. in review. Oceanic Copepods Fine-Tune Their Metabolism During Diel Vertical Migration.</p>
<p>Briefly, <em>Pleuromamma xiphias</em> were collected offshore from the Bermuda Institute of Ocean Sciences (BIOS) during a cruise aboard the R/V Atlantic Explorer from May 20-22, 2019. Net tows were conducted at 12 time points, spaced 4-7 hours apart to target mid-day, early night, mid-night and morning. Nighttime tows (early- and mid-night) were conducted using a 1-m² Reeve net deployed to 200 m depth, with 150 µm mesh size, 20 L cod end, and a miniSTAR-ODDI pressure and depth sensor. Daytime tows (morning and afternoon) were conducted using a 1-m² MOCNESS with 150 µm mesh size and a custom thermally-insulated closing cod with one closing net sampling from 400-600 m. Because the cruise coincided with Tropical Storm Andrea, it was necessary to relocate the ship twice to avoid high winds and continue sampling. The latitude, longitude, date and time (local) for each tow details this relocation. After each tow, copepods were examined under a Leica M205 C stereo microscope to identify adult P. xiphias and determine their gender. Copepods were used immediately for respirometry and excretion measurements.</p>
<p>Water for physiological experiments was obtained daily from 200 m using the rosette on the CTD. It was gravity filtered past a 0.2 µm Supor filter in a Georig 142 mm filter holder and equilibrated to 20°C in an upright incubator. At each time point, up to six copepods were transferred into individual respiration chambers that consisted of 50 mL glass syringes containing an optically sensitive oxygen sensor (OXFOIL: PyroScience, Aachen Germany) and 30 mL of 0.2 µm filtered seawater. Oxygen concentration in each chamber was then measured non-invasively and continuously (every 60 seconds) for approximately 3 hours using two FireSting optical oxygen meters (PyroScience, Aachen Germany). At the end of the experiment, the chambers were visually inspected to ensure that the copepods were still swimming. A 15-mL subsample of water was filtered at a 30º upward angle (to avoid damaging copepods or fecal pellets) through 0.7 µm GFF filters into 15-mL conical vials that had been pre-treated with OPA working reagent (21 mM sodium tetraborate, 0.063 mM sodium sulfite, 50 mL L¹ o-phthalaldehyde in ethanol). This filtered water was refrigerated (4°C) for less than 24 h and then run for ammonium measurements at sea. Ammonium was measured using the OPA (o-phthalaldehyde) method (Holmes et al. 1999). The copepod and any fecal pellets from each chamber were rinsed into a petri dish. Any fecal pellets were counted and photographed under a stereomicroscope. Copepods were rinsed once in DI water and frozen at -80ºC. Frozen copepods were subsequently weighed on a Mettler-Toledo XPR microbalance, dried, and reweighed.</p>
Specified by the Principal Investigator(s)
<p>BCO-DMO Processing:<br />
- converted latitude and longitude from degrees and decimal minutes to decimal degrees;<br />
- added ISO8601 date/time field.</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
Turner fluorometer with Amonium module
Turner fluorometer with Amonium module
PI Supplied Instrument Name: Turner fluorometer with Amonium module Instrument Name: Fluorometer Instrument Short Name:Fluorometer Instrument Description: A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/113/
1-m2 MOCNESS
1-m2 MOCNESS
PI Supplied Instrument Name: 1-m2 MOCNESS PI Supplied Instrument Description:Daytime tows (morning and afternoon) were conducted using a 1-m² MOCNESS with 150 um mesh size and a custom thermally-insulated closing cod with one closing net sampling from 400-600 m. Instrument Name: MOCNESS Instrument Short Name:MOCNESS Instrument Description: The Multiple Opening/Closing Net and Environmental Sensing System or MOCNESS is a family of net systems based on the Tucker Trawl principle. There are currently 8 different sizes of MOCNESS in existence which are designed for capture of different size ranges of zooplankton and micro-nekton Each system is designated according to the size of the net mouth opening and in two cases, the number of nets it carries. The original MOCNESS (Wiebe et al, 1976) was a redesigned and improved version of a system described by Frost and McCrone (1974). (from MOCNESS manual) Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/NETT0097/
PI Supplied Instrument Name: PI Supplied Instrument Description:Water for physiological experiments was obtained daily from 200 m using the rosette on the CTD. 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/
FireSting optical oxygen meters
FireSting optical oxygen meters
PI Supplied Instrument Name: FireSting optical oxygen meters PI Supplied Instrument Description:Oxygen concentration in each chamber was then measured non-invasively and continuously (every 60 seconds) for approximately 3 hours using two FireSting optical oxygen meters (PyroScience, Aachen Germany). Instrument Name: Oxygen Sensor Instrument Short Name:Dissolved Oxygen Sensor Instrument Description: An electronic device that measures the proportion of oxygen (O2) in the gas or liquid being analyzed
miniSTAR-ODDI
miniSTAR-ODDI
PI Supplied Instrument Name: miniSTAR-ODDI PI Supplied Instrument Description:Nighttime tows (early- and mid-night) were conducted using a 1-m² Reeve net deployed to 200 m depth, with 150 um mesh size, 20 L cod end, and a miniSTAR-ODDI pressure and depth sensor. Instrument Name: Pressure Sensor Instrument Short Name:Pressure Sensor Instrument Description: A pressure sensor is a device used to measure absolute, differential, or gauge pressures. It is used only when detailed instrument documentation is not available.
Reeve net
Reeve net
PI Supplied Instrument Name: Reeve net PI Supplied Instrument Description:Nighttime tows (early- and mid-night) were conducted using a 1-m² Reeve net deployed to 200 m depth, with 150 µm mesh size, 20 L cod end, and a miniSTAR-ODDI pressure and depth sensor. Instrument Name: Reeve Net Instrument Short Name:Reeve Net Instrument Description: A Reeve Net is a conventional ring net with a very large acrylic cylindrical cod-end (30 liters) designed to collect fragile gelatinous animals. The net is lowered to a particular depth and then hauled slowly back to the surface (5-10 m/min). Reeve (1981) also described a double net system with no bridle and flotation at the net mouth that is attached to a roller mechanism that rides on a tow wire.
The roller system is locked in place by a pressure release device. Once below a set pressure, the roller
and nets are released and they float slowly up the wire, gently collecting the zooplankton, without being
influenced by the motion of the vessel and associated vertical wire movements. (from Wiebe and Benfield, 2003) Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/NETT0147/
Mettler-Toledo XPR microbalance
Mettler-Toledo XPR microbalance
PI Supplied Instrument Name: Mettler-Toledo XPR microbalance PI Supplied Instrument Description:Frozen copepods were weighed on a Mettler-Toledo XPR microbalance. Instrument Name: scale or balance Instrument Short Name: Instrument Description: Devices that determine the mass or weight of a sample. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB13/
Cruise: AE1910
AE1910
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel
AE1910
Amy Elizabeth Maas
Bermuda Institute of Ocean Sciences
http://datadocs.bco-dmo.org/docs/Zooplankton_Diel_Rhythm/data_docs/AE1910_Cruise_report_ZDR.pdf
Report describing AE1910
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel