http://lod.bco-dmo.org/id/dataset/855732
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
2021-07-15
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Respirometry data for pelagic crustaceans, cephalopods, and fish collected on R/V Sikuliaq cruise SKQ201701S from January to February 2017
2021-07-22
publication
2021-07-22
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-07-22
publication
https://doi.org/10.26008/1912/bco-dmo.855732.1
Brad Seibel
University of South Florida
principalInvestigator
Christopher Neil Roman
University of Rhode Island
principalInvestigator
Karen Wishner
University of Rhode Island
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: Seibel, B., Roman, C., Wishner, K. (2021) Respirometry data for pelagic crustaceans, cephalopods, and fish collected on R/V Sikuliaq cruise SKQ201701S from January to February 2017. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-07-22 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.855732.1 [access date]
Respirometry data for pelagic crustaceans, cephalopods, and fish Dataset Description: Methods and Sampling: <p>This dataset comprises results of respirometry experiments conducted at sea. Experimental animals were collected using either a modified tucker trawl or MOCNESS. Metabolic rates and critical oxygen pressures were measured using published methods (Birk et al., 2018; 2019; Wishner et al., 2018; Seibel et al., 2021). Briefly, individual specimens were placed in darkened sealed chambers filled with 0.2 μm filtered seawater that had been treated with antibiotics (25 mg/L each of streptomycin and actinomycin) to minimize bacterial respiration. The ratio of chamber size to body mass was approximately 1:20. Oxygen content was continuously monitored using Pyroscience Firesting or Presens oxygen meters and fiber optic probes with oxygen-sensitive fluorescent spots. Oxygen meters were calibrated with air-saturated seawater and concentrated Na2SO3 solution (PO2 = 0). Chamber water was mixed with magnetic stirrers (Cole-Parmer Immersible Stirrer EW-04636-50) to ensure homogenous oxygen levels throughout the chamber. Oxygen consumption rates (MO2) were calculated from the slope of PO2 over time. Only linear regressions with an R2 &gt; 0.8 were included. The median MO2 value from non-hypoxic oxygen levels was calculated for each individual. The Pcrit for each individual was calculated using three metrics, including the traditional "breakpoint" method, the "sub-prediction interval (sub-PI)" and the alpha-method.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1459243 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1459243
completed
Brad Seibel
University of South Florida
401-744-4927
College of Marine Science 830 1st St SE
St. Petersburg
FL
33701
USA
seibel@usf.edu
pointOfContact
Christopher Neil Roman
University of Rhode Island
508-274-0232
215 South Ferry Road
Narragansett
RI
02879
USA
croman2@uri.edu
pointOfContact
Karen Wishner
University of Rhode Island
401-874-6402
215 South Ferry Road
Narragansett
RI
02882
USA
kwishner@uri.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Animal_ID
Event
Net_ID
Expt_start_date
Respirometer
Temp
Channel
Volume
Taxa
AphiaID_accepted
ScientificName_accepted
Mass
MO2
msMO2
Pcrit_fixed_width
Pcrit_sub_reg
Pcrit_slide_width
Pcrit_on_duration
Pcrit_sub_reg_corrected
MOCNESS
Pyroscience Firesting FS02-4
Presens Witrox 4 OX11875
Presens Plate Reader SY11000, SDR-547
modified tucker trawl
theme
None, User defined
individual
event
net
date
instrument
water temperature at measurement depth
No BCO-DMO term
volume
taxon
species scientific name (binomial)
mass
O2 consumption
featureType
BCO-DMO Standard Parameters
MOCNESS1
Oxygen Sensor
Oxygen Sensor
plate reader
Tucker Trawl
instrument
BCO-DMO Standard Instruments
SKQ201701S
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: A metabolic index to predict the consequences of climate change for midwater ecosystems
https://osprey.bco-dmo.org/project/663015
Collaborative Research: A metabolic index to predict the consequences of climate change for midwater ecosystems
<p><em>Description from NSF award abstract:</em><br />
With climate change, ocean temperatures are expected to increase which in turn will reduce oxygen availability and increase metabolic oxygen demand in marine organisms. The investigators will conduct shipboard physiological experiments for various marine organisms and determine their distributions in relation to environmental conditions within an oxygen minimum zone (OMZ) in the Eastern Pacific Ocean. The goal will be to model and map a Metabolic Index (MI) to predict how vertical and horizontal distributions for these species might change throughout the world's oceans in the future. The MI is defined as the ratio between environmental oxygen supply and temperature-dependent oxygen demand. Oxygen supply includes both the environmental oxygen concentration across a habitat range and the physiological features of organisms that facilitate oxygen uptake, such as gills and circulatory systems. Thus, the MI will integrate measured tolerance and environmental exposure to low oxygen with environmental data. The investigators will measure tolerance to low oxygen, focusing on under-studied organisms, including the effect of temperature and organism size. They will sample along a natural gradient in oxygen content south of the California Current in the Eastern Pacific. The science team and a videographer will develop a blog about deep-sea biology and climate change using web-based and video technologies. Four graduate students will be funded on this project, and in conjunction with a recently developed course in pelagic ecology, several undergraduates will have the opportunity to participate in seagoing research.</p>
<p>This research fills a critical need for a physiology-based metric that can be used to predict changing marine communities as the oceans warm and hypoxic zones expand. Modern OMZs are extensive and characterized by deep-water (300-800 m) oxygen partial pressures lethal to most marine organisms, yet thriving communities exist there. Climate change is predicted to further deplete oxygen. The investigators will model and map a Metabolic Index (MI) for diverse marine species to help predict how in vertical and horizontal distributions of species may change throughout the world's oceans in the future. The MI will derive oxygen supply and demand data from published and planned measurements of the minimum environmental partial pressure of oxygen to which individual species are exposed (based on their distributions in the water column) and the minimum requirements to support routine aerobic metabolic demand (from shipboard respiration measurements of individuals). During research cruises in the Eastern Pacific along a gradient of OMZ intensity, the investigators will conduct shipboard physiological measurements to determine metabolic demand for understudied mesozooplankton and gelatinous taxa and determine the size- and temperature dependence for diverse species for incorporation into the MI. Vertically-stratified net sampling and in situ photography will identify and characterize unique OMZ community features, such as the lower oxycline biomass peak present in some OMZs and the oxygen-dependence of day and night habitat depths for vertically-migrating species. The MI will be mapped using climatological data to both test and generate hypotheses about the response of oceanic communities to climate change. In preliminary analysis, the MI suggests a metabolic constraint at a MI of ~2 that may act to limit vertical and horizontal habitat ranges.</p>
Metabolic Index
largerWorkCitation
project
eng; USA
oceans
-118.05
-116.5
21.22
22.42
2017-01-22
2017-02-13
Eastern Tropical North Pacific
0
BCO-DMO catalogue of parameters from Respirometry data for pelagic crustaceans, cephalopods, and fish collected on R/V Sikuliaq cruise SKQ201701S from January to February 2017
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/855773.rdf
Name: Animal_ID
Units: unitless
Description: <p>unique identifier for each experimental animal; numbers 008-025 are not included as they were Plate Reader blanks</p>
http://lod.bco-dmo.org/id/dataset-parameter/855774.rdf
Name: Event
Units: unitless
Description: <p>sampling event number from the cruise event log</p>
http://lod.bco-dmo.org/id/dataset-parameter/855775.rdf
Name: Net_ID
Units: unitless
Description: <p>net identifier (combination of gear type + cast number from the cruise event log)</p>
http://lod.bco-dmo.org/id/dataset-parameter/855776.rdf
Name: Expt_start_date
Units: unitless
Description: <p>start date of the experiment; format: YYYY-MM-DD</p>
http://lod.bco-dmo.org/id/dataset-parameter/855777.rdf
Name: Respirometer
Units: unitless
Description: <p>instrument used to obtain measurements (details in “Instruments” section)</p>
http://lod.bco-dmo.org/id/dataset-parameter/855778.rdf
Name: Temp
Units: degrees Celsius
Description: <p>experimental temperature</p>
http://lod.bco-dmo.org/id/dataset-parameter/855779.rdf
Name: Channel
Units: unitless
Description: <p>respirometer channel number (1-4) or well plate ID (A1-D6)</p>
http://lod.bco-dmo.org/id/dataset-parameter/855780.rdf
Name: Volume
Units: liters (L)
Description: <p>water volume (L) of respirometry chamber</p>
http://lod.bco-dmo.org/id/dataset-parameter/855781.rdf
Name: Taxa
Units: unitless
Description: <p>general taxonomic category of experimental animals (e.g. shrimp, squid, etc.)</p>
http://lod.bco-dmo.org/id/dataset-parameter/855782.rdf
Name: AphiaID_accepted
Units: unitless
Description: <p>species AphiaID number from the World Register of Marine Species (WoRMS)</p>
http://lod.bco-dmo.org/id/dataset-parameter/855783.rdf
Name: ScientificName_accepted
Units: unitless
Description: <p>accepted species name from the World Register of Marine Species (WoRMS)</p>
http://lod.bco-dmo.org/id/dataset-parameter/855784.rdf
Name: Mass
Units: milligrams (mg)
Description: <p>mass of experimental animal in milligrams</p>
http://lod.bco-dmo.org/id/dataset-parameter/855785.rdf
Name: MO2
Units: micromoles (umol) per hour
Description: <p>oxygen consumption rate (metabolic rate) in units of umol per hour</p>
http://lod.bco-dmo.org/id/dataset-parameter/855786.rdf
Name: msMO2
Units: micromoles (umol) per gram per hour
Description: <p>mass specific oxygen consumption rate (metabolic rate) in units of umol per gram per hour</p>
http://lod.bco-dmo.org/id/dataset-parameter/855787.rdf
Name: Pcrit_fixed_width
Units: kilopascals (kPa)
Description: <p>breakpoint Pcrit using 10 minute bins if total duration < 1000 minutes and 60 minute bins if total duration > 1000 minutes</p>
http://lod.bco-dmo.org/id/dataset-parameter/855788.rdf
Name: Pcrit_sub_reg
Units: kilopascals (kPa)
Description: <p>sliding bin width based on PO2. Pcrit defined as intersection of conforming line and lower 95% prediction interval bound; outliers removed.</p>
http://lod.bco-dmo.org/id/dataset-parameter/855789.rdf
Name: Pcrit_slide_width
Units: kilopascals (kPa)
Description: <p>sliding bin width based on PO2; Pcrit defined as breakpoint</p>
http://lod.bco-dmo.org/id/dataset-parameter/855790.rdf
Name: Pcrit_on_duration
Units: kilopascals (kPa)
Description: <p>breakpoint Pcrit using PO2 vs duration (biased low)</p>
http://lod.bco-dmo.org/id/dataset-parameter/855791.rdf
Name: Pcrit_sub_reg_corrected
Units: kilopascals (kPa)
Description: <p>Plate Reader only, applies to runs where Pcrit was adjusted to compensate for the poor factory calibration of sensor dots</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
55346
https://darchive.mblwhoilibrary.org/bitstream/1912/27372/1/dataset-855732_zooplankton-metabolic-traits__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.855732.1
download
onLine
dataset
<p>This dataset comprises results of respirometry experiments conducted at sea. Experimental animals were collected using either a modified tucker trawl or MOCNESS. Metabolic rates and critical oxygen pressures were measured using published methods (Birk et al., 2018; 2019; Wishner et al., 2018; Seibel et al., 2021). Briefly, individual specimens were placed in darkened sealed chambers filled with 0.2 μm filtered seawater that had been treated with antibiotics (25 mg/L each of streptomycin and actinomycin) to minimize bacterial respiration. The ratio of chamber size to body mass was approximately 1:20. Oxygen content was continuously monitored using Pyroscience Firesting or Presens oxygen meters and fiber optic probes with oxygen-sensitive fluorescent spots. Oxygen meters were calibrated with air-saturated seawater and concentrated Na2SO3 solution (PO2 = 0). Chamber water was mixed with magnetic stirrers (Cole-Parmer Immersible Stirrer EW-04636-50) to ensure homogenous oxygen levels throughout the chamber. Oxygen consumption rates (MO2) were calculated from the slope of PO2 over time. Only linear regressions with an R2 &gt; 0.8 were included. The median MO2 value from non-hypoxic oxygen levels was calculated for each individual. The Pcrit for each individual was calculated using three metrics, including the traditional "breakpoint" method, the "sub-prediction interval (sub-PI)" and the alpha-method.</p>
Specified by the Principal Investigator(s)
<p><strong>Data Processing</strong>:<br />
Data were processed in R using published tools from Birk (2020). Calculated values of critical oxygen partial pressure (Pcrit) are compared among methods that use different bin sizes and/or definitions of Pcrit, as described below.</p>
<p><strong>Pcrit_fixed_width</strong>: breakpoint Pcrit using 10 minute bins if total duration &lt; 1000 minutes and 60 minute bins if total duration &gt; 1000 minutes.</p>
<p><strong>Pcrit_sub_reg</strong>: sliding bin width based on PO2. Pcrit defined as intersection of conforming line and lower 95% prediction interval bound. Outliers removed.</p>
<p><strong>Pcrit_slide_width</strong>: sliding bin width based on PO2. Pcrit defined as breakpoint.</p>
<p><strong>Pcrit_on_duration</strong>: breakpoint Pcrit using PO2 vs duration (biased low).</p>
<p><strong>Pcrit_sub_reg_corrected</strong>: Plate Reader only - applies to runs where Pcrit was adjusted to compensate for the poor factory calibration of sensor dots.</p>
<p><strong>BCO-DMO Processing:</strong><br />
- replaced "NA"&nbsp;with "nd"&nbsp;(no data);<br />
- renamed fields to comply with BCO-DMO naming conventions;<br />
- converted date to YYYY-MM-DD format;<br />
- changed year of 2027 to 2017 on line 286;<br />
- replaced values of "15? 18?" in the Temp&nbsp;column with "nd".</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
MOCNESS
MOCNESS
PI Supplied Instrument Name: MOCNESS PI Supplied Instrument Description:Experimental animals were collected using either a modified tucker trawl or MOCNESS. Instrument Name: MOCNESS1 Instrument Short Name:MOC1 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. The MOCNESS-1 carries nine 1-m2 nets usually of 335 micrometer mesh and is intended for use with the macrozooplankton. All nets are black to reduce contrast with the background. A motor/toggle release assembly is mounted on the top portion of the frame and stainless steel cables with swaged fittings are used to attach the net bar to the toggle release. A stepping motor in a pressure compensated case filled with oil turns the escapement crankshaft of the toggle release which sequentially releases the nets to an open then closed position on command from the surface. -- from the MOCNESS Operations Manual (1999 + 2003). Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/NETT0097/
Pyroscience Firesting FS02-4
Pyroscience Firesting FS02-4
PI Supplied Instrument Name: Pyroscience Firesting FS02-4 PI Supplied Instrument Description:Pyroscience Firesting FS02-4: four-channel optical oxygen meter 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
Presens Witrox 4 OX11875
Presens Witrox 4 OX11875
PI Supplied Instrument Name: Presens Witrox 4 OX11875 PI Supplied Instrument Description:Presens Witrox 4 OX11875: four-channel optical oxygen meter 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
Presens Plate Reader SY11000, SDR-547
Presens Plate Reader SY11000, SDR-547
PI Supplied Instrument Name: Presens Plate Reader SY11000, SDR-547 PI Supplied Instrument Description:Presens Plate Reader SY11000, SDR-547: optical oxygen meter with 24 wells (75 µl each) Instrument Name: plate reader Instrument Short Name: Instrument Description: Plate readers (also known as microplate readers) are laboratory instruments designed to detect biological, chemical or physical events of samples in microtiter plates. They are widely used in research, drug discovery, bioassay validation, quality control and manufacturing processes in the pharmaceutical and biotechnological industry and academic organizations. Sample reactions can be assayed in 6-1536 well format microtiter plates. The most common microplate format used in academic research laboratories or clinical diagnostic laboratories is 96-well (8 by 12 matrix) with a typical reaction volume between 100 and 200 uL per well. Higher density microplates (384- or 1536-well microplates) are typically used for screening applications, when throughput (number of samples per day processed) and assay cost per sample become critical parameters, with a typical assay volume between 5 and 50 µL per well. Common detection modes for microplate assays are absorbance, fluorescence intensity, luminescence, time-resolved fluorescence, and fluorescence polarization. From: http://en.wikipedia.org/wiki/Plate_reader, 2014-09-0-23.
modified tucker trawl
modified tucker trawl
PI Supplied Instrument Name: modified tucker trawl PI Supplied Instrument Description:Experimental animals were collected using either a modified tucker trawl or MOCNESS. Instrument Name: Tucker Trawl Instrument Short Name:Tucker Trawl Instrument Description: The original Tucker Trawl, a net with a rectangular mouth opening first built in 1951 by G.H. Tucker, was not an opening/closing system, but shortly thereafter it was modified so that it could be opened and closed. The original had a 183 cm by 183 cm flexible rectangular mouth opening 914 cm long net with 1.8 cm stretched mesh for the first 457 cm and 1.3 cm mesh for last 457 cm. 152 cm of coarse plankton or muslin netting lined the end of the net. Tucker designed the net to collect animals associated with the deep scattering layers, principally euphausiids, siphonophores, and midwater fish. (from Wiebe and Benfield, 2003). Currently used Tucker Trawls usually have 1-m2 openings and can have a single net or multiple nets on the frame. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/NETT0161/
Cruise: SKQ201701S
SKQ201701S
R/V Sikuliaq
Community Standard Description
International Council for the Exploration of the Sea
R/V Sikuliaq
vessel
SKQ201701S
Brad Seibel
University of Hawai'i
R/V Sikuliaq
Community Standard Description
International Council for the Exploration of the Sea
R/V Sikuliaq
vessel