Dataset: Siphonophore bulk stable isotopes
Deployment: WF0721

Siphonophore bulk stable isotopes

View Data: For data, See Dataset Metadata Page: https://osprey.bco-dmo.org/dataset/916958

Principal Investigator:

C. Anela Choy (University of California-San Diego, UCSD-SIO)

Scientist:

Elizabeth D. Hetherington (University of California-San Diego, UCSD-SIO)

BCO-DMO Data Manager:

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

Project:

Collaborative research: The effects of predator traits on the structure of oceanic food webs (SiphWeb)

Version:

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Description

Methods & Sampling

Dataset acquisition description

Samples were collected in the central and southern California Current. Most samples were collected in the Monterey Bay region, but a subset of samples were collected in southern California in 2020 and 2021. Samples were collected from between 0 to 3,000 meters depth. Samples were collected on four cruises across three years. All cruises were on the R/V Western Flyer. Dr. Steven Haddock (haddock@mbari.org) was the Chief Scientist on all cruises. Cruises occurred in March 2019 (Cruise ID: WF0319), January 2020 (Cruise ID: WF0120), July 2020 (Cruise ID: WF0720), and July 2021 (Cruise ID: WF0721). Sample locations and dates are provided as columns in the data file.

Siphonophores were collected using three methods: (1) a remotely operated vehicle, (2) blue water diving, and (3) a midwater trawl.

(1) We used the Remotely Operated Vehicle (ROV) Doc Ricketts (https://www.mbari.org/technology/rov-doc-ricketts/) to collect siphonophores, which is an electro-hydraulic vehicle that operates between 200 and 4000 meters. The vehicle was fitted with high-definition video cameras, environmental data instrumentation (e.g. depth, temperature, salinity, and oxygen sensors), and suction and detritus samples to collect in-tact siphonophore specimens. ROV collections occurred during daylight hours.

(2) Siphonophores were collected by blue water diving between 0 and 20 meters during daylight hours. Blue water diving techniques followed the guidelines in the following publication: Haddock, Steven HD, and John N. Heine. "Scientific blue-water diving." (2005). From Haddock and Heine (2005): "In a typical blue-water dive, working divers are connected to a surface platform (and indirectly to each other) by tethers attached to a central hub, which is tended by a safety diver. This hub is connected to a down-line, providing a vertical point of reference. A surface float allows the divers to drift freely through the upper water-column, focusing on their work while the safety diver acts as a buddy for everyone."

(3) A Tucker Trawl with a frame area: 2 square meters (m²), mesh size: 500 micrometers (μm) was towed obliquely for ~2 hours between 900 meters and the surface at night.

Upon collection, siphonophores were identified to the finest taxonomic level, which was either genus or species. For some genera, there are likely undescribed and/or cryptic species (e.g., Apolemia) and for these taxa, genera-level identifications were used. All siphonophores were rinsed with DI water and frozen at -80°C until further processing. Siphonophore tissues were weighed, lyophilized, packaged into tin capsules for bulk isotope analysis, and analyzed at the University of Hawaii's Isotope Geochemistry Facility.

For bulk stable isotope analysis, siphonophore samples were analyzed using a Costech (Valencia, CA, USA) elemental combustion system coupled to a Thermo-Finnigan Delta XP isotope ratio mass spectrometer with N2 standard for nitrogen and Vienna Pee Dee Belemnite for carbon.

A subset of samples was selected for compound-specific isotope analysis of amino acids (CSIA-AA). CSIA-AA was also conducted at the University of Hawaii's Isotope Geochemistry Facility using acid hydrolysis followed by derivatization (see Popp et al. (2007) and Hannides et al. (2013) for details). The CSIA-AA data are available in a separate BCO-DMO dataset (see 'Related Datasets').

Related Resources:
Some of the siphonophores collected in this dataset were also used for metabarcoding. Those data are published Damian-Serrano, et al. (2022) (doi: 10.1371/journal.pone.0267761)

Illumina sequencing data files can be found in the NCBI BioProject PRJNA733192 (https://www.ncbi.nlm.nih.gov/bioproject/733192)

Prey 18S reference database enhancement sequences are available in NCBI (accession numbers between MZ333540 - MZ333629)

Other data, intermediary files, and all code can be found in the GitHub repository: https://github.com/dunnlab/siphweb_metabarcoding (see DOI: doi.org/10.1371/journal.pone.0267761)

Data Processing Description

Dataset Processing Description

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1829812	NSF Division of Ocean Sciences

Instruments

Elemental Analyzer

Supplied Name: Costech (Valencia, CA, USA) elemental combustion system

Supplied Description:

Instrument Type

Generic Name: Elemental Analyzer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB01/

Generic Description:

Instruments that quantify carbon, nitrogen and sometimes other elements by combusting the sample at very high temperature and assaying the resulting gaseous oxides. Usually used for samples including organic material.

Isotope-ratio Mass Spectrometer

Supplied Name: Thermo-Finnigan Delta XP isotope ratio mass spectrometer

Supplied Description:

Instrument Type

Generic Name: Isotope-ratio Mass Spectrometer

Acronym: IR Mass Spec; IRMS

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/

Generic Description:

The Isotope-ratio Mass Spectrometer is a particular type of mass spectrometer used to measure the relative abundance of isotopes in a given sample (e.g. VG Prism II Isotope Ratio Mass-Spectrometer).

Manual Biota Sampler

Supplied Name: blue water diving

Supplied Description:

Siphonophores were collected by blue water diving between 0-20 meters during daylight hours. Blue water diving techniques following the guidelines in the following publication: Haddock, Steven HD, and John N. Heine. "Scientific blue-water diving." (2005).

Instrument Type

Generic Name: Manual Biota Sampler

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/90/

Generic Description:

"Manual Biota Sampler" indicates that a sample was collected in situ by a person, possibly using a hand-held collection device such as a jar, a net, or their hands. This term could also refer to a simple tool like a hammer, saw, or other hand-held tool.

ROV Doc Ricketts

Supplied Name: Remotely Operated Vehicle Doc Ricketts

Supplied Description:

We used the Remotely Operated Vehicle Doc Ricketts (https://www.mbari.org/technology/rov-doc-ricketts/) to collect siphonophores, which is an electro-hydraulic vehicle that operates between 200 and 4000 meters. The vehicle was fitted with high-definition video cameras, environmental data instrumentation (e.g. depth, temperature, salinity, and oxygen sensors), and suction and detritus samples to collect in-tact siphonophore specimens. ROV collections occurred during daylight hours.

Instrument Type

Generic Name: ROV Doc Ricketts

Acronym: Doc Ricketts

Generic Description:

The remotely operated vehicle (ROV) Doc Ricketts is operated by the Monterey Bay Aquarium Research Institute (MBARI). ROV Doc Ricketts is capable of diving to 4000 meters (about 2.5 miles). The R/V Western Flyer is the support vessel for Doc Ricketts and was designed with a center well whose floor can be opened to allow Doc Ricketts to be launched from within the ship into the water below. For a complete description, see: https://www.mbari.org/at-sea/vehicles/remotely-operated-vehicles/rov-doc-ricketts/

Tucker Trawl

Supplied Description:

A Tucker Trawl with a frame area of 2 square meters and a mesh size of 500 micrometers was towed obliquely for ~2h hours between 900 meters and the surface at night.

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

Supplied Name	Supplied description	Supplied Units	Standard Name
Ship	Ship Name	unitless	ship
Chief_Scientist	Chief Scientist Name	unitless	chief_scientist
Cruise_Name	Cruise name, where the format is the ship's initials (e.g., WF for Western Flyer) followed by MMYY (month and year)	unitless	cruise_id
Year	Year of sample collection	unitless	year
Month	Month of sample collection	unitless	month
Family	Taxonomic family of specimen	unitless	family
Genus	Taxonomic genus of specimen	unitless	genus
Best_Taxonomic_ID	Best taxonomic identification of specimen, usually at the genus or species level	unitless	taxon
Depth_m	collection depth; trawl sample depths were the midpoint depths of the trawl, all blue water diving samples were assigned a depth of 10m, which was the average of dive depths; specimens collected with the ROV have discrete collection depths	meters (m)	depth
Latitude	latitude of sample collection (positive values = North)	decimal degrees	lat
Longitude	longitude of sample collection (negative values = West)	decimal degrees	lon
EAweight_mg	mass of the sample analyzed on the Elemental Analyzer	milligrams (mg)	mass
ug_C	mass of carbon detected in the sample by the elemental analyzer	micrograms (ug)	C
d13C	carbon isotope values relative to the international standard Vienna Pee Dee Belemnite	parts per thousand	d13C_bio
ug_N	mass of nitrogen detected in the sample by the elemental analyzer	micrograms (ug)	N
d15N	nitrogen isotope values relative to the international standard N2	parts per thousand	d15N_bio

Database

Contribute Data

Dataset: Siphonophore bulk stable isotopes
Deployment: WF0721

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Siphonophore bulk stable isotopesDeployment: WF0721

Dataset acquisition description

Dataset Processing Description

Dataset: Siphonophore bulk stable isotopes
Deployment: WF0721