http://lod.bco-dmo.org/id/dataset/926850
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)
16S rRNA gene of microorganisms sampled along the Newport Hydrographic (NH) and Trinidad Head (TR) lines, in OR and CA in 2018 and 2019
2024-05-15
publication
2024-05-15
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2025-02-27
publication
https://doi.org/10.26008/1912/bco-dmo.926850.1
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) 16S rRNA gene of microorganisms sampled along the Newport Hydrographic (NH) and Trinidad Head (TR) lines, in OR and CA in 2018 and 2019. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-05-15 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.926850.1 [access date]
16S rRNA gene of microorganisms Dataset Description: Methods and Sampling: <p>Transects ranged from 24 to 86 km in length were sampled along the Newport Hydrographic (NH) line as well as the Trinidad Head (TR) line during the winters (February-March) and summers (July-August) of 2018 and 2019 (winter 2018 transect sample size was n=2 per location due to weather days while summer 2018 – summer 2019, n=4-5). Located off Newport, Oregon, the NH Line has been sampled since 1961 (Peterson and Miller, 1975), while the TR line off northern California has been sampled since 2007.</p>
<p>DNA sampling for microbes was carried out from surface (5-10 meters depth) seawater samples (500-1000 mL, n=2 per station, 6 stations per transect), collected by CTD, that were size fractionated on 47 mm 1.6 µm GF/A filters (Whatman) followed by 47 mm 0.2 µm Supor polyethersulfone filters (Pall Corporation)&nbsp; using a peristaltic pump. Filter membranes were moved to bead-beater tubes and frozen immediately at -20 ˚C and stored at -80 ˚C. DNA extraction was done using the DNeasy Plant Tissue Mini Kit (Qiagen) with the following modifications. 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. PCR was performed in triplicate on 1 ng of DNA with the primer pair 515F‐Y/806R amplified the 16S rRNA V4 hypervariable region with conditions as published (Parada et al. 2016) using golay barcodes on the forward primers as in the EMP protocols. Reactions were performed with the QuantaBio 5Prime HotMasterMix (Qiagen Beverly, MA, USA). The Agilent High Sensitivity Kit in the Bioanalyzer (Agilent Technologies, Waldbronn, Germany) confirmed amplicon size. Triplicate PCR reactions from each sample were pooled then purified by magnetic beads. Each final pooled sample was paired-end sequenced with Illumina MiSeq v.3 (Illumina, San Diego, USA).&nbsp;&nbsp;&nbsp;&nbsp;</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
organism
collection_date
depth
env_broad_scale
env_local_scale
env_medium
geo_loc_name
sampling_lat
sampling_lon
size_frac
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_filename
fasta_filename2
theme
None, User defined
NCBI BioProject accession
NCBI BioSample accession
No BCO-DMO term
sample identification
taxon
date
depth
sample description
region
latitude
longitude
sample fraction (includes size fractions)
NCBI SRA run accession (SRR)
NCBI SRA study accession (SRP)
seq_descrip
instrument
instrument model
datatype
file_name
featureType
BCO-DMO Standard Parameters
CTD Sea-Bird
Niskin bottle
instrument
BCO-DMO Standard Instruments
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
-125.18113333
-124.00338333
41.05433333
44.6607
2018-02-16
2019-07-25
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 16S rRNA gene of microorganisms sampled along the Newport Hydrographic (NH) and Trinidad Head (TR) lines, in OR and CA in 2018 and 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/927651.rdf
Name: bioproject_accession
Units: unitless
Description: <p>NCBI Bioproject accession ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/927652.rdf
Name: biosample_accession
Units: unitless
Description: <p>NCBI Biosample accession ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/927653.rdf
Name: message
Units: unitless
Description: <p>NCBI message</p>
http://lod.bco-dmo.org/id/dataset-parameter/927654.rdf
Name: sample_name
Units: unitless
Description: <p>Submitter sample name</p>
http://lod.bco-dmo.org/id/dataset-parameter/927655.rdf
Name: organism
Units: unitless
Description: <p>Organism name by submitter</p>
http://lod.bco-dmo.org/id/dataset-parameter/927656.rdf
Name: collection_date
Units: unitless
Description: <p>Collection date of organism</p>
http://lod.bco-dmo.org/id/dataset-parameter/927657.rdf
Name: depth
Units: meter (m)
Description: <p>Sampling depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/927658.rdf
Name: env_broad_scale
Units: unitless
Description: <p>Broad-scale environmental context</p>
http://lod.bco-dmo.org/id/dataset-parameter/927659.rdf
Name: env_local_scale
Units: unitless
Description: <p>Local-scale environmental context</p>
http://lod.bco-dmo.org/id/dataset-parameter/927660.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/927661.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/927662.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/927663.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/927664.rdf
Name: size_frac
Units: unitless
Description: <p>Selected size fraction</p>
http://lod.bco-dmo.org/id/dataset-parameter/927665.rdf
Name: sra_run_accession
Units: unitless
Description: <p>NCBI SRA run accession ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/927666.rdf
Name: sra_study_accession
Units: unitless
Description: <p>NCBI study accession ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/927667.rdf
Name: object_status
Units: unitless
Description: <p>Status of object</p>
http://lod.bco-dmo.org/id/dataset-parameter/927668.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/927669.rdf
Name: title
Units: unitless
Description: <p>Library title</p>
http://lod.bco-dmo.org/id/dataset-parameter/927670.rdf
Name: library_strategy
Units: unitless
Description: <p>Sequencing library strategy</p>
http://lod.bco-dmo.org/id/dataset-parameter/927671.rdf
Name: library_source
Units: unitless
Description: <p>Source of sequencing library</p>
http://lod.bco-dmo.org/id/dataset-parameter/927672.rdf
Name: library_selection
Units: unitless
Description: <p>Selection used for sequencing library</p>
http://lod.bco-dmo.org/id/dataset-parameter/927673.rdf
Name: library_layout
Units: unitless
Description: <p>single or paired end sequencing reads</p>
http://lod.bco-dmo.org/id/dataset-parameter/927674.rdf
Name: platform
Units: unitless
Description: <p>Sequencing platform manufacturer</p>
http://lod.bco-dmo.org/id/dataset-parameter/927675.rdf
Name: instrument_model
Units: unitless
Description: <p>Sequencer model</p>
http://lod.bco-dmo.org/id/dataset-parameter/927676.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/927677.rdf
Name: filetype
Units: unitless
Description: <p>File type</p>
http://lod.bco-dmo.org/id/dataset-parameter/927678.rdf
Name: fasta_filename
Units: unitless
Description: <p>Forward reads file name</p>
http://lod.bco-dmo.org/id/dataset-parameter/927679.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
57823
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/df5e0be5-e40d-41f0-bb98-5da36e1cd54e/content
download
https://doi.org/10.26008/1912/bco-dmo.926850.1
download
onLine
dataset
<p>Transects ranged from 24 to 86 km in length were sampled along the Newport Hydrographic (NH) line as well as the Trinidad Head (TR) line during the winters (February-March) and summers (July-August) of 2018 and 2019 (winter 2018 transect sample size was n=2 per location due to weather days while summer 2018 – summer 2019, n=4-5). Located off Newport, Oregon, the NH Line has been sampled since 1961 (Peterson and Miller, 1975), while the TR line off northern California has been sampled since 2007.</p>
<p>DNA sampling for microbes was carried out from surface (5-10 meters depth) seawater samples (500-1000 mL, n=2 per station, 6 stations per transect), collected by CTD, that were size fractionated on 47 mm 1.6 µm GF/A filters (Whatman) followed by 47 mm 0.2 µm Supor polyethersulfone filters (Pall Corporation)&nbsp; using a peristaltic pump. Filter membranes were moved to bead-beater tubes and frozen immediately at -20 ˚C and stored at -80 ˚C. DNA extraction was done using the DNeasy Plant Tissue Mini Kit (Qiagen) with the following modifications. 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. PCR was performed in triplicate on 1 ng of DNA with the primer pair 515F‐Y/806R amplified the 16S rRNA V4 hypervariable region with conditions as published (Parada et al. 2016) using golay barcodes on the forward primers as in the EMP protocols. Reactions were performed with the QuantaBio 5Prime HotMasterMix (Qiagen Beverly, MA, USA). The Agilent High Sensitivity Kit in the Bioanalyzer (Agilent Technologies, Waldbronn, Germany) confirmed amplicon size. Triplicate PCR reactions from each sample were pooled then purified by magnetic beads. Each final pooled sample was paired-end sequenced with Illumina MiSeq v.3 (Illumina, San Diego, USA).&nbsp;&nbsp;&nbsp;&nbsp;</p>
Specified by the Principal Investigator(s)
<p>Amplicon sequence variants (ASVs) of seawater samples were identified based on 16S rRNA gene sequence reads that were processed using <em>dada2</em> and <em>phyloseq</em>. Sequences were quality controlled using <em>filterAndTrim()</em> with truncLen set to 190 (forward reads) and 160 (reverse reads), maxEE was set to 3, and maxN set to 0 to eliminate low quality base calls. Forward and reverse primers were trimmed from all reads. Error learning, sample inference, and merging of paired-end reads were done with <em>dada2</em> default settings to yield unique amplicon sequence variants (ASVs). Chimeric ASVs were removed with the "consensus" method. The reference database "RefSeq-RDP16S_v2_May2018" was used to assign taxonomy to the ASVs. <em>phyloseq</em> was used to connect ASV sequence counts per sample to taxonomic data and metadata. Sequence abundances were standardized to the median sequencing depth of all samples (“standardized relative abundance”) without rarefying. Raw sequence data can be accessed from the NCBI Sequence Read Archive at <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA999694/">https://www.ncbi.nlm.nih.gov/bioproject/PRJNA999694/</a>.</p>
Specified by the Principal Investigator(s)
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
PI Supplied Instrument Name: Instrument Name: CTD Sea-Bird Instrument Short Name:CTD Sea-Bird Instrument Description: A Conductivity, Temperature, Depth (CTD) sensor package from SeaBird Electronics. This instrument designation is used when specific make and model are not known or when a more specific term is not available in the BCO-DMO vocabulary. Refer to the dataset-specific metadata for more information about the specific CTD used. More information from: http://www.seabird.com/ Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/130/
PI Supplied Instrument Name: 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/