Dataset: Zooplankton metabolic traits

Name: Respirometry data for pelagic crustaceans, cephalopods, and fish collected on R/V Sikuliaq cruise SKQ201701S from January to February 2017
Published: 2021-07-22
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.855732.1

Spatial Extent: N:22.42 E:-116.5 S:21.22 W:-118.05

Temporal Extent: 2017-01-22 - 2017-02-13

Project:

Collaborative Research: A metabolic index to predict the consequences of climate change for midwater ecosystems (Metabolic Index)

Principal Investigator:

Brad Seibel (University of South Florida, USF)

Co-Principal Investigator:

Christopher Neil Roman (University of Rhode Island, URI)

Karen Wishner (University of Rhode Island, URI-GSO)

Contact:

Brad Seibel (University of South Florida, USF)

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2021-07-22

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Respirometry data for pelagic crustaceans, cephalopods, and fish collected on R/V Sikuliaq cruise SKQ201701S from January to February 2017

Abstract:

This dataset comprises results of respirometry experiments conducted at sea using pelagic crustaceans, cephalopods, and fish collected on R/V Sikuliaq cruise SKQ201701S from January to February 2017. Experimental animals were collected using either a modified tucker trawl or MOCNESS.

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2021-07-22	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.855732.1	2021-07-22

Methods & Sampling

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 > 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.

Data Processing Description

Data Processing:
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.

Pcrit_fixed_width: breakpoint Pcrit using 10 minute bins if total duration < 1000 minutes and 60 minute bins if total duration > 1000 minutes.

Pcrit_sub_reg: sliding bin width based on PO2. Pcrit defined as intersection of conforming line and lower 95% prediction interval bound. Outliers removed.

Pcrit_slide_width: sliding bin width based on PO2. Pcrit defined as breakpoint.

Pcrit_on_duration: breakpoint Pcrit using PO2 vs duration (biased low).

Pcrit_sub_reg_corrected: Plate Reader only - applies to runs where Pcrit was adjusted to compensate for the poor factory calibration of sensor dots.

BCO-DMO Processing:
- replaced "NA" with "nd" (no data);
- renamed fields to comply with BCO-DMO naming conventions;
- converted date to YYYY-MM-DD format;
- changed year of 2027 to 2017 on line 286;
- replaced values of "15? 18?" in the Temp column with "nd".

Data Files

File
zoop_metabolic_traits.csv (Comma Separated Values (.csv), 54.05 KB) MD5:beb14050ceef6aec20ebf0ff4f510e14 Primary data file for dataset ID 855732

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1459243
NSF Division of Ocean Sciences	OCE-1459243

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
SKQ201701S		2017-01-19	R/V Sikuliaq	Brad Seibel (Chief Scientist)	data info

Instruments

MOCNESS1

Supplied Name: MOCNESS

Supplied Description:

Experimental animals were collected using either a modified tucker trawl or MOCNESS.

Instrument Type

Generic Name: MOCNESS1

Acronym: MOC1

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/NETT0097/

Generic 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).

Oxygen Sensor

Supplied Name: Pyroscience Firesting FS02-4

Supplied Description:

Pyroscience Firesting FS02-4: four-channel optical oxygen meter

Instrument Type

Generic Name: Oxygen Sensor

Acronym: Dissolved Oxygen Sensor

Generic Description:

An electronic device that measures the proportion of oxygen (O2) in the gas or liquid being analyzed

Oxygen Sensor

Supplied Name: Presens Witrox 4 OX11875

Supplied Description:

Presens Witrox 4 OX11875: four-channel optical oxygen meter

Instrument Type

Generic Name: Oxygen Sensor

Acronym: Dissolved Oxygen Sensor

Generic Description:

An electronic device that measures the proportion of oxygen (O2) in the gas or liquid being analyzed

plate reader

Supplied Name: Presens Plate Reader SY11000, SDR-547

Supplied Description:

Presens Plate Reader SY11000, SDR-547: optical oxygen meter with 24 wells (75 µl each)

Instrument Type

Generic Name: plate reader

Generic 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.

Tucker Trawl

Supplied Name: modified tucker trawl

Supplied Description:

Experimental animals were collected using either a modified tucker trawl or MOCNESS.

Instrument Type

Generic Name: Tucker Trawl

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/NETT0161/

Generic 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.

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
Animal_ID	unique identifier for each experimental animal; numbers 008-025 are not included as they were Plate Reader blanks	unitless	individual
Event	sampling event number from the cruise event log	unitless	event
Net_ID	net identifier (combination of gear type + cast number from the cruise event log)	unitless	net
Expt_start_date	start date of the experiment; format: YYYY-MM-DD Format: %Y-%m-%d	unitless	date
Respirometer	instrument used to obtain measurements (details in “Instruments” section)	unitless	instrument
Temp	experimental temperature	degrees Celsius	temp
Channel	respirometer channel number (1-4) or well plate ID (A1-D6)	unitless	no_bcodmo_term
Volume	water volume (L) of respirometry chamber	liters (L)	volume
Taxa	general taxonomic category of experimental animals (e.g. shrimp, squid, etc.)	unitless	taxon
AphiaID_accepted	species AphiaID number from the World Register of Marine Species (WoRMS)	unitless	species
ScientificName_accepted	accepted species name from the World Register of Marine Species (WoRMS)	unitless	species
Mass	mass of experimental animal in milligrams	milligrams (mg)	mass
MO2	oxygen consumption rate (metabolic rate) in units of umol per hour	micromoles (umol) per hour	O2_consum
msMO2	mass specific oxygen consumption rate (metabolic rate) in units of umol per gram per hour	micromoles (umol) per gram per hour	O2_consum
Pcrit_fixed_width	breakpoint Pcrit using 10 minute bins if total duration < 1000 minutes and 60 minute bins if total duration > 1000 minutes	kilopascals (kPa)	no_bcodmo_term
Pcrit_sub_reg	sliding bin width based on PO2. Pcrit defined as intersection of conforming line and lower 95% prediction interval bound; outliers removed.	kilopascals (kPa)	no_bcodmo_term
Pcrit_slide_width	sliding bin width based on PO2; Pcrit defined as breakpoint	kilopascals (kPa)	no_bcodmo_term
Pcrit_on_duration	breakpoint Pcrit using PO2 vs duration (biased low)	kilopascals (kPa)	no_bcodmo_term
Pcrit_sub_reg_corrected	Plate Reader only, applies to runs where Pcrit was adjusted to compensate for the poor factory calibration of sensor dots	kilopascals (kPa)	no_bcodmo_term

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Dataset: Zooplankton metabolic traits