http://lod.bco-dmo.org/id/dataset/926841
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
2024-05-06
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Salp and pteropod associated microorganisms from the Western Edge of the Gulf Stream sampled in September 2019.
2024-05-06
publication
2024-05-06
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2025-02-27
publication
https://doi.org/10.26008/1912/bco-dmo.926841.1
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) Salp and pteropod associated microorganisms from the Western Edge of the Gulf Stream sampled in September 2019. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-05-06 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.926841.1 [access date]
16S rRNA sequencing salp and pteropod microorganisms Dataset Description: Methods and Sampling: <p>Collected from the western edge of the Gulf Stream (26°43′93″ N, 79° 59′15″ W) in September 2019, 5–8&nbsp;km east of West Palm Beach, Florida. All samples were collected during daylight in the upper 15 m. Sampling was done by hand.</p>
<p>Jars with animals and jars with seawater were brought on the deck of a 10&nbsp;m dive vessel for processing. Within 30 min of divers surfacing, samples were archived or processed as follows. Salps and pteropods were gently poured onto a metal sieve then rinsed with 0.2&nbsp;μm filtered seawater. Each gut was then removed with dissecting scissors, avoiding as much of the gelatinous tissue as possible. Guts were placed into sterile bead-beating tubes with 0.55 and 0.25 mm sterile glass beads and stored on dry ice until archiving at −80°C in a shore-based laboratory. Salp faecal pellets were sampled from different salp specimens incubated in jars for approximately 1-h after collection. Faecal pellets were collected on a mesh sieve (500 μm), rinsed with 0.2&nbsp;μm filtered seawater, then stored as above. Jars containing seawater collected near sampled animals were transported on blue ice to the shore-based laboratory. For flow cytometry samples, 2&nbsp;ml of seawater was fixed at a final concentration of 0.125% TEM grade glutaraldehyde (Tousimis), incubated at room temperature for 10&nbsp;min, then flash frozen in ethanol cooled with dry ice. Seawater DNA samples were taken by peristaltic pumping onto 0.2&nbsp;μm membrane filters and were stored on dry ice until archiving at −80°C.</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
message
sample_name
sample_title
organism
collection_date
depth
env_broad_scale
env_local_scale
env_medium
geo_loc_name
sampling_lat
sampling_lon
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
filename
filename2
theme
None, User defined
NCBI BioProject accession
NCBI BioSample accession
No BCO-DMO term
sample identification
sample description
taxon
date
depth
region
latitude
longitude
NCBI SRA run accession (SRR)
NCBI SRA study accession (SRP)
seq_descrip
instrument
instrument model
datatype
file_name
featureType
BCO-DMO Standard Parameters
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
-79.9875
-79.9875
26.7425
26.7425
2019-09-15
2019-09-15
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 Salp and pteropod associated microorganisms from the Western Edge of the Gulf Stream sampled in September 2019.
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/927611.rdf
Name: bioproject_accession
Units: unitless
Description: <p>NCBI Bioproject accession ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/927612.rdf
Name: biosample_accession
Units: unitless
Description: <p>NCBI Biosample accession ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/927613.rdf
Name: message
Units: unitless
Description: <p>NCBI message</p>
http://lod.bco-dmo.org/id/dataset-parameter/927614.rdf
Name: sample_name
Units: unitless
Description: <p>Submitter sample name</p>
http://lod.bco-dmo.org/id/dataset-parameter/927615.rdf
Name: sample_title
Units: unitless
Description: <p>Sample accession title</p>
http://lod.bco-dmo.org/id/dataset-parameter/927616.rdf
Name: organism
Units: unitless
Description: <p>Organism name by submitter</p>
http://lod.bco-dmo.org/id/dataset-parameter/927617.rdf
Name: collection_date
Units: unitless
Description: <p>Collection date of organism</p>
http://lod.bco-dmo.org/id/dataset-parameter/927618.rdf
Name: depth
Units: feet
Description: <p>Sampling depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/927619.rdf
Name: env_broad_scale
Units: unitless
Description: <p>Broad-scale environmental context</p>
http://lod.bco-dmo.org/id/dataset-parameter/927620.rdf
Name: env_local_scale
Units: unitless
Description: <p>Local-scale environmental context</p>
http://lod.bco-dmo.org/id/dataset-parameter/927621.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/927622.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/927623.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/927624.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/927625.rdf
Name: sra_run_accession
Units: unitless
Description: <p>NCBI SRA run accession ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/927626.rdf
Name: sra_study_accession
Units: unitless
Description: <p>NCBI study accession ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/927627.rdf
Name: object_status
Units: unitless
Description: <p>Status of object</p>
http://lod.bco-dmo.org/id/dataset-parameter/927628.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/927629.rdf
Name: title
Units: unitless
Description: <p>Library title</p>
http://lod.bco-dmo.org/id/dataset-parameter/927630.rdf
Name: library_strategy
Units: unitless
Description: <p>Sequencing library strategy</p>
http://lod.bco-dmo.org/id/dataset-parameter/927631.rdf
Name: library_source
Units: unitless
Description: <p>Source of sequencing library</p>
http://lod.bco-dmo.org/id/dataset-parameter/927632.rdf
Name: library_selection
Units: unitless
Description: <p>Selection used for sequencing library</p>
http://lod.bco-dmo.org/id/dataset-parameter/927633.rdf
Name: library_layout
Units: unitless
Description: <p>single or paired end sequencing reads</p>
http://lod.bco-dmo.org/id/dataset-parameter/927634.rdf
Name: platform
Units: unitless
Description: <p>Sequencing platform manufacturer</p>
http://lod.bco-dmo.org/id/dataset-parameter/927635.rdf
Name: instrument_model
Units: unitless
Description: <p>Sequencer model</p>
http://lod.bco-dmo.org/id/dataset-parameter/927636.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/927637.rdf
Name: filetype
Units: unitless
Description: <p>File type</p>
http://lod.bco-dmo.org/id/dataset-parameter/927638.rdf
Name: filename
Units: unitless
Description: <p>Forward reads file name</p>
http://lod.bco-dmo.org/id/dataset-parameter/927639.rdf
Name: 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
9888
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/99fb28e0-0e42-4962-b144-6725682a23ff/content
download
https://doi.org/10.26008/1912/bco-dmo.926841.1
download
onLine
dataset
<p>Collected from the western edge of the Gulf Stream (26°43′93″ N, 79° 59′15″ W) in September 2019, 5–8&nbsp;km east of West Palm Beach, Florida. All samples were collected during daylight in the upper 15 m. Sampling was done by hand.</p>
<p>Jars with animals and jars with seawater were brought on the deck of a 10&nbsp;m dive vessel for processing. Within 30 min of divers surfacing, samples were archived or processed as follows. Salps and pteropods were gently poured onto a metal sieve then rinsed with 0.2&nbsp;μm filtered seawater. Each gut was then removed with dissecting scissors, avoiding as much of the gelatinous tissue as possible. Guts were placed into sterile bead-beating tubes with 0.55 and 0.25 mm sterile glass beads and stored on dry ice until archiving at −80°C in a shore-based laboratory. Salp faecal pellets were sampled from different salp specimens incubated in jars for approximately 1-h after collection. Faecal pellets were collected on a mesh sieve (500 μm), rinsed with 0.2&nbsp;μm filtered seawater, then stored as above. Jars containing seawater collected near sampled animals were transported on blue ice to the shore-based laboratory. For flow cytometry samples, 2&nbsp;ml of seawater was fixed at a final concentration of 0.125% TEM grade glutaraldehyde (Tousimis), incubated at room temperature for 10&nbsp;min, then flash frozen in ethanol cooled with dry ice. Seawater DNA samples were taken by peristaltic pumping onto 0.2&nbsp;μm membrane filters and were stored on dry ice until archiving at −80°C.</p>
Specified by the Principal Investigator(s)
<p>DNA was extracted with the DNeasy Plant Tissue Mini Kit (Qiagen) with the following modifications. Salp guts, salp fecal pellets, and pteropod tissues were ground with a sterile disposable pestle (Axygen, Tewksbury, USA) for 3 minutes prior to extraction. All samples, including seawater, 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 a final concentration of 2 mg/mL Proteinase K (VWR Chemicals, Solon, OH, USA) for 1 hour at 55 ˚C, and then incubated with a final concentration of 0.9 mg/mL RNase A 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. Reactions were performed with 0.5-2 ng of DNA using the QuantaBio 5Prime HotMasterMix (Qiagen Beverly, MA, USA). To overcome PCR inhibition in salp samples, bovine serum albumin (BSA) was added to the salp PCRs, see details below. The Agilent Bioanalyzer High Sensitivity Kit (Agilent Technologies, Waldbronn, Germany) confirmed amplicon size. Triplicate PCRs from each sample were pooled, cleaned with magnetic beads, and paired-end sequenced (2 x 300 bp) with Illumina MiSeq v.3 (Illumina, San Diego, USA). Sequences were deposited in the Sequence Read Archive (SRA).</p>
Specified by the Principal Investigator(s)
* Merged biosample and SRA run file
* Removed no data columns from files
* Adjusted parameters to comply with database 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