http://lod.bco-dmo.org/id/dataset/926093
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
2024-04-26
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
High-throughput sequencing of the 16S rRNA gene, microscopy, and flow cytometry of pyrosome-associated microorganisms compared to seawater sampled during a Pyrosoma atlanticum bloom in the Northern California Current System in July 2018.
2024-05-14
publication
2024-05-14
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2025-02-27
publication
https://doi.org/10.26008/1912/bco-dmo.926093.1
Anne W. Thompson
Portland State University
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: Thompson, A. W. (2025) High-throughput sequencing of the 16S rRNA gene, microscopy, and flow cytometry of pyrosome-associated microorganisms compared to seawater sampled during a Pyrosoma atlanticum bloom in the Northern California Current System in July 2018. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-05-14 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.926093.1 [access date]
16S rRNA sequencing pyrosome-associated microorganisms Dataset Description: Methods and Sampling: <p>Pyrosomes and seawater were collected from the NCC, off the Oregon Coast, in July 2018, near the peak of a multiyear bloom of <em>P. atlanticum.</em> Samples were collected from the R/V Sally Ride (SR1810) along the Newport Hydrographic Line. Station D5 (Cast 20, 44.652141N; 125.117573W) was sampled on July 9, 2018 in the presence of a strong temperature gradient in the top 20 meters and a chlorophyll peak at 17 meters. Station D3 (Cast 26, 44.651756N; 124.589313W) was sampled on July 11, 2018 in the presence of a mixed layer depth of 15 meters and a chlorophyll peak at the base of the mixed layer.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1851412 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1851412
completed
Anne W. Thompson
Portland State University
503-725-8052
PO Box 751
Portland
OR
97201
USA
awt@pdx.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
bioproject_accession
biosample_accession
sample_name
sra_sample_accession
sample_accession_title
organism_name
organism_taxonomy_id
organism_taxonomy_name
keywords
biosample_package
collection_date
env_broad_scale
env_local_scale
env_medium
geo_loc_name
host
sampling_lat
sampling_lon
depth
host_length
source_material_id
status
when
access
date_publication
date_last_update
date_submission_date
sra_run_accession
sra_study_accession
object_status
library_ID
title
library_strategy
library_source
library_selection
library_layout
platform
instrument_model
design_description
filetype
fasta_filename1
fasta_filename2
Niskin CTD Rosette for seawater
MOCNESS for animals
Niskin CTD Rosette for seawater
theme
None, User defined
NCBI BioProject accession
NCBI BioSample accession
sample identification
NCBI SRA Sample accession (SRS)
sample description
taxon
taxon_code
date
region
latitude
longitude
depth
length
No BCO-DMO term
ISO_DateTime_UTC
NCBI SRA run accession (SRR)
NCBI SRA study accession (SRP)
seq_descrip
instrument
instrument model
datatype
file_name
featureType
BCO-DMO Standard Parameters
CTD - profiler
MOCNESS
Niskin bottle
instrument
BCO-DMO Standard Instruments
SR1810
service
Deployment Activity
Northern California Current waters
place
Locations
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: Comparative feeding by gelatinous grazers on microbial prey
https://osprey.bco-dmo.org/project/751083
Collaborative Research: Comparative feeding by gelatinous grazers on microbial prey
<p><em>NSF Award Abstract:</em><br />
The oceans are dominated by microscopic plants and animals (microorganisms) that are at the base of the food web and drive energy and carbon cycles on global scales. Soft jellylike animals called gelatinous grazers specialize in feeding on microorganisms using nets made out of mucus. Gelatinous grazers are abundant in the ocean and have high feeding rates on microorganisms so could have a very strong influence on the abundance and diversity of microorganisms and could change how oceanic food webs are currently understood. However, gelatinous grazers are very fragile and patchy in their distributions so it has been difficult to determine the magnitude and dynamics of these important predator-prey relationships on a meaningful scale using traditional approaches, thus they have typically been disregarded in food web studies. Learning more about the predator-prey relationship between gelatinous grazers and microorganisms will improve understanding of the structure, mechanics, and dynamics of the ocean's food web, which is a critical economic and ecosystem resource on Earth. This project is determining grazing rates by gelatinous animals on microbes to inform food web models. The project also trains students to communicate, disseminate, and interpret scientific findings. These broader impacts goals will be attained through partnerships at the University of Oregon (Applied Scientific Communication) and Portland State University (Advanced Technical Writing), training of 1 PhD student, 2 undergraduates, and 4 science communication interns, and development of a week-long workshop and establish student mentorship relationships towards production of communication products.</p>
<p>The project integrates laboratory and oceanographic approaches to address several specific aspects of the predator-prey relationship between gelatinous grazers and ocean microorganisms. Five distinct types of gelatinous grazers, each with different feeding morphologies and life history, will be studied in an oceanographic setting with an abundant and diverse natural microbial population. These target organisms include pelagic tunicates (salps, appendicularians, doliolods and pyrosomes) and thecosome pteropods. The approach quantifies: 1) grazing rates in the natural ocean environment, 2) particle selectivity with a focus on size and shape and, 3) the morphological and hydrodynamic properties of feeding that underlie the measured grazing rates and particle selection. The project uses a variety of techniques including sampling via SCUBA diving, laboratory experiments, high speed/high resolution videography, flow cytometry, and DNA sequencing techniques.</p>
Gelatinous Grazer Feeding
largerWorkCitation
project
eng; USA
oceans
Northern California Current waters
-125.117573
-124.589313
44.651756
44.652141
2018-07-09
2018-07-11
North Pacific Subtropical Gyre, at a field site 3 nautical miles offshore of Kona, Hawai’i (19.710746 N, 22.75 W) & Sars Centre for Marine Molecular Biology in Bergen, Norway
0
BCO-DMO catalogue of parameters from High-throughput sequencing of the 16S rRNA gene, microscopy, and flow cytometry of pyrosome-associated microorganisms compared to seawater sampled during a Pyrosoma atlanticum bloom in the Northern California Current System in July 2018.
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/927357.rdf
Name: bioproject_accession
Units: unitless
Description: <p>NCBI Bioproject accession ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/927358.rdf
Name: biosample_accession
Units: unitless
Description: <p>NCBI Biosample accession ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/927359.rdf
Name: sample_name
Units: unitless
Description: <p>Submitter sample name</p>
http://lod.bco-dmo.org/id/dataset-parameter/927360.rdf
Name: sra_sample_accession
Units: unitless
Description: <p>NCBI SRA sample accession ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/927361.rdf
Name: sample_accession_title
Units: unitless
Description: <p>Sample accession title</p>
http://lod.bco-dmo.org/id/dataset-parameter/927362.rdf
Name: organism_name
Units: unitless
Description: <p>Organism name by submitter</p>
http://lod.bco-dmo.org/id/dataset-parameter/927363.rdf
Name: organism_taxonomy_id
Units: unitless
Description: <p>NCBI Taxonomy ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/927364.rdf
Name: organism_taxonomy_name
Units: unitless
Description: <p>NCBI organism name related to taxonomy id</p>
http://lod.bco-dmo.org/id/dataset-parameter/927365.rdf
Name: keywords
Units: unitless
Description: <p>NCBI biosample keywords</p>
http://lod.bco-dmo.org/id/dataset-parameter/927366.rdf
Name: biosample_package
Units: unitless
Description: <p>NCBI biosample attribute package and package version</p>
http://lod.bco-dmo.org/id/dataset-parameter/927367.rdf
Name: collection_date
Units: unitless
Description: <p>Collection date of organism</p>
http://lod.bco-dmo.org/id/dataset-parameter/927368.rdf
Name: env_broad_scale
Units: unitless
Description: <p>Broad-scale environmental context</p>
http://lod.bco-dmo.org/id/dataset-parameter/927369.rdf
Name: env_local_scale
Units: unitless
Description: <p>Local-scale environmental context</p>
http://lod.bco-dmo.org/id/dataset-parameter/927370.rdf
Name: env_medium
Units: unitless
Description: <p>Material displaced by the entity at time of sampling</p>
http://lod.bco-dmo.org/id/dataset-parameter/927371.rdf
Name: geo_loc_name
Units: unitless
Description: <p>Geographic location of the origin of the sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/927372.rdf
Name: host
Units: unitless
Description: <p>Host name</p>
http://lod.bco-dmo.org/id/dataset-parameter/927373.rdf
Name: sampling_lat
Units: decimal degrees
Description: <p>Latitude of sampling location, south is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/927374.rdf
Name: sampling_lon
Units: decimal degrees
Description: <p>Longitude of sampling location, west is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/927375.rdf
Name: depth
Units: meter (m)
Description: <p>Sampling depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/927376.rdf
Name: host_length
Units: centimeter (cm)
Description: <p>Length of the subject</p>
http://lod.bco-dmo.org/id/dataset-parameter/927377.rdf
Name: source_material_id
Units: unitless
Description: <p>Unique identifier assigned to a material sample used for extracting nucleic acids, and subsequent sequencing.</p>
http://lod.bco-dmo.org/id/dataset-parameter/927378.rdf
Name: status
Units: unitless
Description: <p>Sample NCBI status (live)</p>
http://lod.bco-dmo.org/id/dataset-parameter/927379.rdf
Name: when
Units: unitless
Description: <p>When status set</p>
http://lod.bco-dmo.org/id/dataset-parameter/927380.rdf
Name: access
Units: unitless
Description: <p>Accessibility: public</p>
http://lod.bco-dmo.org/id/dataset-parameter/927381.rdf
Name: date_publication
Units: unitless
Description: <p>Date of publication at NCBI</p>
http://lod.bco-dmo.org/id/dataset-parameter/927382.rdf
Name: date_last_update
Units: unitless
Description: <p>Data of last update at NCBI</p>
http://lod.bco-dmo.org/id/dataset-parameter/927383.rdf
Name: date_submission_date
Units: unitless
Description: <p>Date of submisison at NCBI</p>
http://lod.bco-dmo.org/id/dataset-parameter/927384.rdf
Name: sra_run_accession
Units: unitless
Description: <p>NCBI SRA run accession ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/927385.rdf
Name: sra_study_accession
Units: unitless
Description: <p>NCBI study accession ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/927386.rdf
Name: object_status
Units: unitless
Description: <p>Status of object</p>
http://lod.bco-dmo.org/id/dataset-parameter/927387.rdf
Name: library_ID
Units: unitless
Description: <p>Unique identifier for the sequencing library (can be the sample name repeated).</p>
http://lod.bco-dmo.org/id/dataset-parameter/927388.rdf
Name: title
Units: unitless
Description: <p>Library title</p>
http://lod.bco-dmo.org/id/dataset-parameter/927389.rdf
Name: library_strategy
Units: unitless
Description: <p>Sequencing library strategy</p>
http://lod.bco-dmo.org/id/dataset-parameter/927390.rdf
Name: library_source
Units: unitless
Description: <p>Source of sequencing library</p>
http://lod.bco-dmo.org/id/dataset-parameter/927391.rdf
Name: library_selection
Units: unitless
Description: <p>Selection used for sequencing library</p>
http://lod.bco-dmo.org/id/dataset-parameter/927392.rdf
Name: library_layout
Units: unitless
Description: <p>single or paired end sequencing reads</p>
http://lod.bco-dmo.org/id/dataset-parameter/927393.rdf
Name: platform
Units: unitless
Description: <p>Sequencing platform manufacturer</p>
http://lod.bco-dmo.org/id/dataset-parameter/927394.rdf
Name: instrument_model
Units: unitless
Description: <p>Sequencer model</p>
http://lod.bco-dmo.org/id/dataset-parameter/927395.rdf
Name: design_description
Units: unitless
Description: <p>Description explaining how this library was prepared and sequenced</p>
http://lod.bco-dmo.org/id/dataset-parameter/927396.rdf
Name: filetype
Units: unitless
Description: <p>File type</p>
http://lod.bco-dmo.org/id/dataset-parameter/927397.rdf
Name: fasta_filename1
Units: unitless
Description: <p>Forward reads file name</p>
http://lod.bco-dmo.org/id/dataset-parameter/927398.rdf
Name: fasta_filename2
Units: unitless
Description: <p>Reverse reads file name</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
12453
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/a3bf5b37-2187-45d6-9f40-ece7be8f5e52/content
download
https://doi.org/10.26008/1912/bco-dmo.926093.1
download
onLine
dataset
<p>Pyrosomes and seawater were collected from the NCC, off the Oregon Coast, in July 2018, near the peak of a multiyear bloom of <em>P. atlanticum.</em> Samples were collected from the R/V Sally Ride (SR1810) along the Newport Hydrographic Line. Station D5 (Cast 20, 44.652141N; 125.117573W) was sampled on July 9, 2018 in the presence of a strong temperature gradient in the top 20 meters and a chlorophyll peak at 17 meters. Station D3 (Cast 26, 44.651756N; 124.589313W) was sampled on July 11, 2018 in the presence of a mixed layer depth of 15 meters and a chlorophyll peak at the base of the mixed layer.</p>
Specified by the Principal Investigator(s)
<p>DNA extraction was done using the DNeasy Plant Tissue Mini Kit (Qiagen) with the following modifications. Pyrosome tissue was ground with a sterile pestle (Axygen, Tewksbury, USA) for 3 minutes prior to extraction. Seawater and pyrosome samples were lysed by bead beating with 0.55 mm and 0.25 mm sterile glass beads at 30 Hz for 2 minutes after addition of lysis buffer, freeze-fractured 3 times, incubated with Proteinase K (VWR Chemicals, Solon, OH, USA) at 20 mg/mL for 1 hour at 55 ˚C, and incubated with RNase A at 100 mg/mL for 10 minutes at 65 ˚C. To minimize amplification of eukaryotic host DNA, the primer pair 515F‐Y/806R was chosen to amplify the 16S rRNA V4 hypervariable region with conditions as published. 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, USA).</p>
<p>&nbsp;</p>
Specified by the Principal Investigator(s)
* Converted NCBI biosample file to flat file format
* Merged biosample and SRA run file
* Removed no data columns from files
* Adjusted parameters to comply with databaser requirements (spaces, characters, etc)
* Converted date to ISO format
* Split lat/lon column into their own columns
Specified by BCO-DMO Data Managers
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
Niskin CTD Rosette for seawater
Niskin CTD Rosette for seawater
PI Supplied Instrument Name: Niskin CTD Rosette for seawater Instrument Name: CTD - profiler Instrument Short Name: Instrument 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. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/130/
MOCNESS for animals
MOCNESS for animals
PI Supplied Instrument Name: MOCNESS for animals Instrument Name: MOCNESS Instrument Short Name:MOCNESS 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. 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) Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/NETT0097/
Niskin CTD Rosette for seawater
Niskin CTD Rosette for seawater
PI Supplied Instrument Name: Niskin CTD Rosette for seawater Instrument Name: Niskin bottle Instrument Short Name:Niskin bottle Instrument 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. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/
Cruise: SR1810
SR1810
R/V Sally Ride
Community Standard Description
International Council for the Exploration of the Sea
R/V Sally Ride
vessel
SR1810
Robert K. Cowen
Oregon State University
R/V Sally Ride
Community Standard Description
International Council for the Exploration of the Sea
R/V Sally Ride
vessel