Dataset: Deep-sea larvae for microbiome study
Deployment: YK10-11

This dataset provides the sampling locations and identifications for larvae collected near three deep-sea hydrothermal vent fields and used in a microbiome study by Carrier et al. (2021). This dataset provides metadata for larval and microbiome genetic sequence data in another repository (Carrier et al., 2021, doi.org/10.5061/dryad.sqv9s4n18). The data table is structured as a Darwin Core occurrence table so that it can be harvested by the Ocean Biodiversity Information System (OBIS) and Global Biodiversity Information Facility (GBIF). In addition to the data table, photographs are provided for some of the specimens. A .zip file of images is attached containing the .JPG files referenced by column "associatedMedia".

Larvae were collected near three different hydrothermal vent fields with locality, Location, and waterBody (N. Pacific) specified in the data: East Pacific Rise, 9 50 N vent field, Tica vent site at N EPR; Mariana Back-Arc, Snail and Archaean vent fields in Mariana Trough; and Pescadero Basin, Auka vent field in Gulf of California.

Methods & Sampling

Dataset acquisition description

Larval collection:
These larvae were collected near hydrothermal vent fields on the East Pacific Rise (EPR 9°50'N vent field), on the Mariana Back-Arc Spreading Center (near Snail or Archaean vent fields), and in Pescadero Basin (Auka vent field) in the Gulf of California. The EPR specimens were from McLane WTS-LV50 plankton pumps deployed on-axis near Tica vent site on LADDER 3 cruise AT15-26 in 2007. The pump sampled for 24 hr over a 63 micron mesh at a rate of 30 L/min at a position about 3 meters above bottom. The Mariana specimens were from the same plankton pumps with same configuration deployed on-site or off-site but within 300 m of active hydrothermal vents on R/V Yokosuka cruise YK10-11 in 2010. The Pescadero specimens were from the suction (slurp) sampler on ROV Hercules on E/V Nautilus cruise NA091 in 2017. The slurp sampled for 10 min over a 63 micron mesh at a rate of ~100 L/min at a position about 1 meter above bottom, while the ROV was parked on-site at an active vent ("intensive sampling station", or ISS). ISS 2 was during ROV dive H1657, and ISS 4 was during ROV dive H1658.

We acknowledge the sample collection permits CONAPESCA PPFE/DGOPA-010/17 and INEGI: Autorización EG0072017 associated to the Diplomatic Note number SRE 17-1087 (CTC/06727/17).

Shipboard sample processing:
Pump and slurp samples were processed within an hour upon recovery on deck, with many specimens alive. The sample was washed off the filter using 95% non-denatured ethanol into a 250 mL jar (brand new or rinsed with ethanol, but was not autoclaved).

Laboratory sorting and morphological identification:
Portions of the sample were extracted with a wide-mouthed pipette into a petri dish for sorting under a dissecting scope at magnifications up to 50X (although most tools were rinsed with ethanol, none were autoclaved). Specimens were sorted into vials by major taxa (i.e., all the gastropod larvae together), in some cases with separate vials for those retained on 300um or 63um sieve. Vials were brand new or rinsed with ethanol, but were not autoclaved. Individuals were identified to morphotypes at lowest taxonomic level. Some morphotypes contain morphologically indistinguishable larvae from multiple species (e.g., polychaete nectochaetes).

Specimens selected for DNA extraction:
We selected specimens in several major taxonomic groups (gastropods, polychaetes, crustaceans, and a bivalve) for DNA extraction. The amount of time the larval specimens had been stored in ethanol at the time of DNA extraction was ~10, ~7, and ~1 yrs, respectively, for EPR, Mariana, and Pescadero specimens. Only the Mariana specimens had been stored at 4 degrees C, while the others were at room temperature. Working in a laminar flow hood, we used sterile techniques to place 25 individuals from EPR and 25 individuals from Mariana into separate 1.5 mL vials with 95% ethanol. We thank Diana Franks for helping with sterile techniques. Pescadero specimens were provided in 2 vials each with 5 individuals of the same morphotype using sterile tools but not in a laminar flow hood.

DNA extraction and amplification are described by Carrier et al. (2021), and 28S rRNA larval genetic sequences and 16S rRNA bacterial genetic sequence data are in the Dryad repository (Carrier et al., 2021, doi.org/10.5061/dryad.sqv9s4n18). The 28S larval sequences were compared to those in the NCBI GenBank database using a BLAST search to assist with matching morphotypes to lowest taxonomic level. Results from the BLAST search were insufficient to provide additional taxonomic resolution; therefore, the 28S genetic results were primarily used as support for the morphological identification. We'd like to thank Bethany Fleming for conducting the BLAST searches.

Additional genetic evidence to assist with larval identification:
We'd like to thank Dr. Hiroka Hidaka, Dr. Shigeaki Kojima, and Dr. Hiromi Watanabe for providing histone 3 and Dr. Florence Pradillon for providing cytochrome oxidase subunit 1 (CO1) sequences for other Mariana larval specimens from the same collections. The Canadian Centre for DNA Barcoding provided CO1 sequences for other Pescadero specimens from the same collections; these results may be viewed in the Barcode of Life Data System (BOLD) Public Data Portal using the project search PESPL.

Data Processing Description

Dataset Processing Description

Data Processing:
The raw data table was created in a Google spreadsheet which was imported directly into a script that removed extraneous columns, added an asterisk to 6 of the TubeIDs, constrained the latitude and longitude to 4 decimal places, and exported the table to a comma-separated values file: https://github.com/sbeaulieu/EPR-traits/blob/master/subset_Google_Sheet_BCODMO_Beaulieu_Carrier.R. The data table is structured as a Darwin Core occurrence table so that it can be harvested by the Ocean Biodiversity Information System (OBIS) and Global Biodiversity Information Facility (GBIF). Note for the column linking to the microbiome genetic sequence data in the Dryad repository, we considered using the Darwin Core term associatedOrganisms but found other studies in which the link to microbiome data was made using an Occurrence Core with an extension for ResourceRelationships.

More information about this dataset deployment

Funding

Award Number	Funding Source
DEB-1558904	NSF Division of Environmental Biology
OCE-0424953	NSF Division of Ocean Sciences
OCE-1028862	NSF Division of Ocean Sciences
OCE-1829773	NSF Division of Ocean Sciences

Instruments

McLane Large Volume Pumping System WTS-LV

Supplied Description:

Instrument Type

Generic Name: McLane Large Volume Pumping System WTS-LV

Acronym: WTS-LV

Generic Description:

The WTS-LV is a Water Transfer System (WTS) Large Volume (LV) pumping instrument designed and manufactured by McLane Research Labs (Falmouth, MA, USA). It is a large-volume, single-event sampler that collects suspended and dissolved particulate samples in situ.

Ambient water is drawn through a modular filter holder onto a 142-millimeter (mm) membrane without passing through the pump. The standard two-tier filter holder provides prefiltering and size fractioning. Collection targets include chlorophyll maximum, particulate trace metals, and phytoplankton. It features different flow rates and filter porosity to support a range of specimen collection. Sampling can be programmed to start at a scheduled time or begin with a countdown delay. It also features a dynamic pump speed algorithm that adjusts flow to protect the sample as material accumulates on the filter. Several pump options range from 0.5 to 30 liters per minute, with a max volume of 2,500 to 36,000 liters depending on the pump and battery pack used. The standard model is depth rated to 5,500 meters, with a deeper 7,000-meter option available. The operating temperature is -4 to 35 degrees Celsius.

The WTS-LV is available in four different configurations: Standard, Upright, Bore Hole, and Dual Filter Sampler. The high-capacity upright WTS-LV model provides three times the battery life of the standard model. The Bore-Hole WTS-LV is designed to fit through a narrow opening such as a 30-centimeter borehole. The dual filter WTS-LV features two vertical intake 142 mm filter holders to allow simultaneous filtering using two different porosities.

Microscope - Optical

Supplied Name: dissecting scope

Supplied Description:

Instrument Type

Generic Name: Microscope - Optical

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB05/

Generic Description:

Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of visible light. Includes conventional and inverted instruments. Also called a "light microscope".

ROV Hercules

Supplied Name:

Supplied Description:

ROV Hercules multi-chamber slurp sampler was used to collect specimens

Instrument Type

Generic Name: ROV Hercules

Generic Description:

ROV Hercules is operated via E/V Nautilus. Hercules is outfitted with features that allow it to perform intricate tasks, including two manipulator arms, a variety of sensors and samplers, a high-definition video camera, several LED lights, and high-resolution mapping tools. The submersible receives power from the surface through a fiber-optic cable, which also transmits data and video, to allow pilots located in the shipboard control van to "fly" the ROV in any direction through the use of its six thrusters. Other sensors located on Hercules measure pressure, depth, water temperature, oxygen concentration, and salinity to accommodate requests from scientists both onboard and onshore. Hercules is equipped with multiple cameras, including the high-definition video camera that allows for real-time telepresence.

The ROV is built to withstand pressures at a depth of 4,000 meters with more than 6,000 pound-force per square inch (psi) for up to three days. See more: https://nautiluslive.org/tech/rov-hercules

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
TubeID	Identifier for the tube containing a single larval specimen for DNA extraction. An asterisk indicates the 6 EPR specimens lost during preparation for sequencing.	unitless	tube_num
Location	A spatial region, using regions from the InterRidge Vents Database Ver. 3.4 https://doi.org/10.1594/PANGAEA.917894. Darwin Core term https://dwc.tdwg.org/terms/#location based on Dublin Core term http://purl.org/dc/terms/Location	unitless	site
waterBody	The name of the water body in which the Location occurs, corresponding to ocean in the InterRidge Vents Database Ver. 3.4 https://doi.org/10.1594/PANGAEA.917894. Darwin Core term http://rs.tdwg.org/dwc/terms/waterBody	unitless	site
locality	The specific description of the place near the sampling event, using names of vent fields and sites in the InterRidge Vents Database Ver. 3.4 https://doi.org/10.1594/PANGAEA.917894	unitless	site
habitat	We describe the habitat as "hydrothermal vent" ENVO term http://purl.obolibrary.org/obo/ENVO_00000215 for those taxa for which we are confident that the adults live at a hydrothermal vent, otherwise NotDetermined. We are not describing the sampling event habitat per se, thus deviating from the definition of Darwin Core term http://rs.tdwg.org/dwc/terms/habitat	unitless	site_descrip
Deployment_Fraction	Numbered deployment (pump mooring or ROV station) with sorting fraction indicated for some samples to help identify the vial into which the specimen was sorted	unitless	sample_descrip
eventID	An identifier for the set of information associated with a sampling event. For the EPR and Mariana specimens, the eventID is built from a cruise identifier and the deployment; for the Pescadero specimens the eventID is the E/V Nautilus sample identifier. Darwin Core term http://rs.tdwg.org/dwc/terms/eventID	unitless	event
decimalLatitude	The geographic latitude in decimal degrees of the sampling near the locality. Positive values are north of the Equator, negative values are south of it. Darwin Core term http://rs.tdwg.org/dwc/terms/decimalLatitude	degrees	lat
decimalLongitude	The geographic longitude in decimal degrees of the sampling near the locality. Positive values are east of the Greenwich Meridian, negative values are west of it. Darwin Core term http://rs.tdwg.org/dwc/terms/decimalLongitude	degrees	lon
Bottom_Depth_Meters	Depth below sea level of the seafloor under the sampling event	meters (m)	depth_bottom
minimumDepthInMeters	The lesser depth of a range of depth below sea level for the sampling event. Darwin Core term http://rs.tdwg.org/dwc/terms/minimumDepthInMeters	meters (m)	depth
maximumDepthInMeters	The greater depth of a range of depth below sea level for the sampling event. Darwin Core term http://rs.tdwg.org/dwc/terms/maximumDepthInMeters	meters (m)	depth
eventDate	The date of the sampling event. Darwin Core term http://rs.tdwg.org/dwc/terms/eventDate. Format: YYYY-MM-DD	unitless	date
Higher_level_taxon_name	Higher level taxonomic name either Bivalvia, Crustacea, Gastropoda, or Polychaeta	unitless	taxon
Lowest_level_taxon_name_or_morphotype	Name used to identify the taxon or morphogroup to the lowest level, not necessarily a scientific name	unitless	taxon
scientificName	Name from World Register of Marine Species at the lowest level that matches the Lowest_level_taxon_name_or_morphotype. Darwin Core term http://rs.tdwg.org/dwc/terms/scientificName	unitless	taxon
scientificNameID	Machine-readable Life Science Identifier (LSID) that pairs the AphiaID from World Register of Marine Species to the scientificName. Darwin Core term http://rs.tdwg.org/dwc/terms/scientificNameID	unitless	taxon_code
occurrenceID	A unique identifier for the Occurrence record to be provided to OBIS and GBIF. The occurrenceID concatenates the eventID with the TubeID. Darwin Core term http://rs.tdwg.org/dwc/terms/occurrenceID	unitless	sample
occurrenceStatus	A statement about the presence of the taxon in the Occurrence record, using controlled vocabulary term present. Darwin Core term http://rs.tdwg.org/dwc/terms/occurrenceStatus	unitless	site_descrip
lifeStage	The life stage of the specimen at the time the Occurrence was recorded, using biological entity development stage terms larvae, zoeae, and juvenile from controlled vocabulary http://vocab.nerc.ac.uk/collection/S11/current/. Darwin Core term http://rs.tdwg.org/dwc/terms/lifeStage	unitless	stage
basisOfRecord	The nature of the Occurrence record, using controlled vocabulary term PreservedSpecimen. Darwin Core term http://rs.tdwg.org/dwc/terms/basisOfRecord	unitless	instrument
associatedSequences	Link to the larval 28S genetic sequence data in the Dryad repository doi:10.5061/dryad.sqv9s4n18 with specimen identifier, associated with the taxon in the Occurrence record. Darwin Core term http://rs.tdwg.org/dwc/terms/associatedSequences	unitless	sequence
microbiome_16S_Dryad	Link to the microbiome 16S genetic sequence data in the Dryad repository doi:10.5061/dryad.sqv9s4n18 with specimen identifier	unitless	accession_number
associatedMedia	A list (concatenated and separated) of filenames of images associated with the Occurrence. Filenames often include specimen identifier and magnification. Darwin Core term http://rs.tdwg.org/dwc/terms/associatedMedia	unitless	file_name

Database

Contribute Data

Dataset: Deep-sea larvae for microbiome studyDeployment: YK10-11

Dataset acquisition description

Dataset Processing Description

Dataset: Deep-sea larvae for microbiome study
Deployment: YK10-11