Dataset: Microorganisms associated with doliolids
Deployment: AT42-13

16S rRNA sequencing doliolids associated microorganisms

View Data: For data, See Dataset Metadata Page: https://www.bco-dmo.org/dataset/926299

Principal Investigator:

Anne W. Thompson (Portland State University, PSU)

Contact:

Anne W. Thompson (Portland State University, PSU)

BCO-DMO Data Manager:

Karen Soenen (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

Collaborative Research: Comparative feeding by gelatinous grazers on microbial prey (Gelatinous Grazer Feeding)

Version:

Deployment Synonyms:

S19

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Description

Methods & Sampling

Dataset acquisition description

Samples were collected during daylight from the R/V Atlantis (AGOR-25) along the Newport Hydrographic (NH) Line at station “NH5” (N 44° 39.084’, W 125° 7.151’) on July 22nd as well as along the Trinidad Head (TR) Line at stations “TR1” (N 41° 3.467, W 124° 16.016) and “TR3” (N 41° 3.448, W 124° 26.7) on July 17th and 19th, respectively.

Doliolids were sampled using a modified coupled Multiple Opening and Closing Net and Environmental Sensing System (MOCNESS). Doliolids were rinsed three times with 0.2 µm filtered seawater to remove unattached microbes, collected in a 1-mL sterile bead-beater tube containing 0.55- and 0.25-mm beads, and then frozen at -80 °C.

Data Processing Description

Dataset Processing Description

Seawater and doliolid samples were lysed by beadbeating with 0.55 mm and 0.25 mm sterile glass beads at 30 Hz for 2 min after addition of lysis buffer, freeze-fractured three times, incubated with Proteinase K (VWR Chemicals, Solon, OH) at 20 mg/mL for 1 h at 55 ˚C, and incubated with RNase A at 100 mg/mL for 10 min at 65˚C. The primer pair 515F‐Y/806R was chosen to amplify the 16S rRNA V4 hypervariable region. Reactions were performed with 0.5-2 ng of DNA using the QuantaBio 5Prime HotMasterMix (Qiagen Beverly, MA USA). The Agilent High Sensitivity Kit in the Bioanalyzer (Agilent Technologies, Waldbronn, Germany) confirmed amplicon size. Triplicate reactions from each sample were pooled and paired-end sequenced with Illumina MiSeq v.3 (Illumina, San Diego, CA). Raw sequence data are available in the Sequence Read Archive Project # PRJNA1055560.

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1851412	NSF Division of Ocean Sciences

Instruments

CTD - profiler

Supplied Name: Niskin CTD Rosette for seawater collection

Supplied Description:

Instrument Type

Generic Name: CTD - profiler

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/130/

Generic Description:

The Conductivity, Temperature, Depth (CTD) unit is an integrated instrument package designed to measure the conductivity, temperature, and pressure (depth) of the water column. The instrument is lowered via cable through the water column. It permits scientists to observe the physical properties in real-time via a conducting cable, which is typically connected to a CTD to a deck unit and computer on a ship. The CTD is often configured with additional optional sensors including fluorometers, transmissometers and/or radiometers. It is often combined with a Rosette of water sampling bottles (e.g. Niskin, GO-FLO) for collecting discrete water samples during the cast.

This term applies to profiling CTDs. For fixed CTDs, see https://www.bco-dmo.org/instrument/869934.

MOCNESS

Supplied Name: MOCNESS for animal collection

Supplied Description:

Instrument Type

Generic Name: MOCNESS

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. 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) This designation is used when the specific type of MOCNESS (number and size of nets) was not specified by the contributing investigator.

Niskin bottle

Supplied Name: Niskin CTD Rosette for seawater collection

Supplied Description:

Instrument Type

Generic Name: Niskin bottle

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/

Generic 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.

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
bioproject_accession	NCBI Bioproject accession ID	unitless	BioProject
biosample_accession	NCBI Biosample accession ID	unitless	BioSample
sample_name	Submitter sample name	unitless	sample
sra_sample_accession	NCBI SRA sample accession ID	unitless	SRA_sample
sample_accession_title	Sample accession title	unitless	sample_descrip
organism_name	Organism name by submitter	unitless	taxon
organism_taxonomy_id	NCBI Taxonomy ID	unitless	taxon_code
organism_taxonomy_name	NCBI organism name related to taxonomy id	unitless	taxon_code
keyword	NCBI biosample keywords	unitless	sample_descrip
biosample_package	NCBI biosample attribute package and package version	unitless	sample_descrip
collection_date	Collection date of organism	unitless	date
depth	Sampling depth	meter (m)	depth
env_broad_scale	Broad-scale environmental context	unitless	sample_descrip
env_local_scale	Local-scale environmental context	unitless	sample_descrip
env_medium	Material displaced by the entity at time of sampling	unitless	sample_descrip
geo_loc_name	Geographic location of the origin of the sample	unitless	region
sampling_lat	Latitude of sampling location, south is negative	decimal degrees	lat
sampling_lon	Longitude of sampling location, west is negative	decimal degrees	lon
size_frac	Selected size fraction	unitless	samp_fraction
host	Host name	unitless	taxon
source_material_id	Unique identifier assigned to a material sample used for extracting nucleic acids, and subsequent sequencing.	unitless	sample
status	Sample NCBI status (live)	unitless	no_bcodmo_term
when	When status set	unitless	no_bcodmo_term
access	Accessibility: public	unitless	no_bcodmo_term
publication_date	Date of publication at NCBI	unitless	ISO_DateTime_UTC
date_last_update	Data of last update at NCBI	unitless	ISO_DateTime_UTC
date_submission_date	Date of submisison at NCBI	unitless	ISO_DateTime_UTC

Database

Contribute Data

Dataset: Microorganisms associated with doliolids
Deployment: AT42-13

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Microorganisms associated with doliolidsDeployment: AT42-13

Dataset acquisition description

Dataset Processing Description

Dataset: Microorganisms associated with doliolids
Deployment: AT42-13