http://lod.bco-dmo.org/id/dataset/997408
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
2026-04-22
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Sequence data accession numbers originating from seawater homarine addition experiments conducted on R/V Rachel Carson RC0078 cruise in the Salish Sea in June 2022
2026-04-22
publication
2026-04-22
revision
BCO-DMO Linked Data URI
2026-04-22
creation
http://lod.bco-dmo.org/id/dataset/997408
Anitra E. Ingalls
University of Washington
principalInvestigator
Oscar A. Sosa
University of Puget Sound
principalInvestigator
Katherine Heal
Pacific Northwest National Laboratory
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: Sosa, O. A., Ingalls, A. E., Heal, K. (2026) Sequence data accession numbers originating from seawater homarine addition experiments conducted on R/V Rachel Carson RC0078 cruise in the Salish Sea in June 2022. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-04-22 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/997408 [access date]
Homarine response experiments RC0078 Dataset Description: Methods and Sampling: <p>CTD data were collected in the Salish Sea on the R/V Rachel Carson, cruise RC0078 in June 2022.</p>
<p>Seawater was transferred to acid-clean, blue-tinted, 5-L polycarbonate carboys for acclimation in a deck incubator with flow-through surface seawater. A set of three carboys were supplied with 0.1 mM carbon as homarine and three other unamended carboys served as control group. We incubated samples for 3.5 hours and proceeded to concentrate the microbial fraction by filtering each through a 47 mm-diameter, 0.22 µm pore-size polycarbonate membrane with a peristaltic pump. The filters were flash-frozen in liquid nitrogen at sea and were transferred to -80°C storage in the lab.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2125886 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2125886
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2124712 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2124712
onGoing
Anitra E. Ingalls
University of Washington
206-221-6748
School of Oceanography Box 355351 4333 Brooklyn Ave NE
Seattle
WA
98195
USA
aingalls@u.washington.edu
pointOfContact
Oscar A. Sosa
University of Puget Sound
1500 N. Warner St.
Tacoma
WA
98416
USA
ososa@pugetsound.edu
pointOfContact
Katherine Heal
Pacific Northwest National Laboratory
School of Oceanography Box 355351 4333 Brooklyn Ave NE
Seattle
WA
98195
USA
kheal@uw.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Cruise
Station
Cast
Depth
Date
Latitude
Longitude
treatment_type
accession_sra_url
accession_number
Illumina NovaSeq 6000
Sea-Bird SBE9 CTD profiler
deck incubator
theme
None, User defined
Cruise identfier
station
cast
depth
date
latitude
longitude
experiment id
external_link
NCBI BioSample accession
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
CTD Sea-Bird SBE 911plus
Shipboard Incubator
instrument
BCO-DMO Standard Instruments
RC0078
service
Deployment Activity
Seattle, WA
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: Resolving the production and fate of nitrogenous metabolites in the surface ocean
https://osprey.bco-dmo.org/project/858734
Collaborative Research: Resolving the production and fate of nitrogenous metabolites in the surface ocean
<p><em>NSF Award Abstract:</em><br />
Photosynthetic microbes provide food for nearly all other life in the ocean. Their metabolism produces organic molecules called metabolites that can leak out of cells, be intentionally excreted into seawater, or be released during cell death. Once outside the cell, these metabolites are the basis for specific interactions among microbes and determine community structure and activity. Yet, current understanding of metabolites in the ocean is limited by a historical lack of ability to measure them. The work proposed here will expand current knowledge of metabolite structures, concentrations, and production rates using recently developed analytical methods. These methods have already led to the discovery that homarine, a substituted pyridine first found in lobster in 1933, is the most abundant detectable metabolite in microbial communities of the North Pacific Ocean. While homarine is known as a predator deterrent, osmoprotectant, methyl donor, and antibiofouling agent, studies of its role in microbial community dynamics are lacking. The work proposed will clarify the role of homarine in the ocean’s microbial communities. This work will create an open-source metabolite database that will serve the broader field of metabolomics, a growing area in environmental, engineering, and medical sciences. This collaboration will also promote the careers of a graduate student and a postdoctoral researcher as well as an early career professor from an underrepresented group at a primarily undergraduate institution (PUI). Undergraduates from both institutions will contribute to project development and implementation, local cruises on the R.V. Carson, lab work, and dissemination of results. This research will be integrated into a curriculum-based research experience for undergraduates in a 200-level genetics course at the PUI, University of Puget Sound.</p>
<p>The proposed work will carry out field studies and laboratory experiments to test the hypothesis that metabolites are quantitatively significant forms of carbon and nitrogen flowing through microbial communities. The identity, quantity, and production rates of metabolites will also be determined. For homarine, the enzymes and organisms responsible for its transformations will be determined. Specific proposed activities will 1) Quantify nitrogenous metabolite pools and their net production rates (particulate and dissolved) in phytoplankton cultures and in marine surface water communities; 2) Isolate homarine consuming heterotrophic bacteria and use mutagenesis techniques, transcriptomics, and stable isotope assisted metabolomics to annotate genes and characterize the biochemical reactions involved in the degradation of homarine; 3) Carry out incubations of stable isotope labeled homarine in phytoplankton cultures, heterotrophic bacterial cultures sensitive to homarine, and natural communities to quantitatively evaluate the effect of homarine on growth, track homarine through metabolic pathways, and determine the kinetics of homarine uptake; 4) Identify homarine consumers and biochemical pathways for homarine use in the environment by mining existing environmental metatranscriptomes for homarine catabolism genes. The combination of these approaches will provide better understanding of the flow of nitrogen containing metabolites through marine microbial ecosystems. Results from this work will be disseminated through peer reviewed open-source publications as well as presentations to the scientific community and the general public.</p>
<p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p>
Nitrogenous Metabolites
largerWorkCitation
project
eng; USA
biota
oceans
Seattle, WA
-122.991667
-122.991667
48.249167
48.249167
2022-06-05
2022-06-05
0
BCO-DMO catalogue of parameters from Sequence data accession numbers originating from seawater homarine addition experiments conducted on R/V Rachel Carson RC0078 cruise in the Salish Sea in June 2022
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/997436.rdf
Name: Cruise
Units: unitless
Description: <p>Cruise ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/997437.rdf
Name: Station
Units: unitless
Description: <p>Station number</p>
http://lod.bco-dmo.org/id/dataset-parameter/997438.rdf
Name: Cast
Units: unitless
Description: <p>Cast number of CTD collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/997439.rdf
Name: Depth
Units: meters
Description: <p>Depth of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/997441.rdf
Name: Date
Units: unitless
Description: <p>Date of sample collection (UTC)</p>
http://lod.bco-dmo.org/id/dataset-parameter/997442.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Latitude, positive is North</p>
http://lod.bco-dmo.org/id/dataset-parameter/997444.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Longitude, negative is West</p>
http://lod.bco-dmo.org/id/dataset-parameter/997446.rdf
Name: treatment_type
Units: unitless
Description: <p>Experiment identifier that indicates carboy number and whether carboy was supplied with 0.1 mM carbon as homarine or whether it served as a control; identifiers are control 1, control 2, control 3, homarine 1, homarine 2, and homarine 3.</p>
http://lod.bco-dmo.org/id/dataset-parameter/997447.rdf
Name: accession_sra_url
Units: unitless
Description: <p>External link to the SRA linked to Biosample</p>
http://lod.bco-dmo.org/id/dataset-parameter/997448.rdf
Name: accession_number
Units: unitless
Description: <p>Biosample accession identifier</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
https://osprey.bco-dmo.org/dataset/997408/data/download
download
onLine
dataset
<p>CTD data were collected in the Salish Sea on the R/V Rachel Carson, cruise RC0078 in June 2022.</p>
<p>Seawater was transferred to acid-clean, blue-tinted, 5-L polycarbonate carboys for acclimation in a deck incubator with flow-through surface seawater. A set of three carboys were supplied with 0.1 mM carbon as homarine and three other unamended carboys served as control group. We incubated samples for 3.5 hours and proceeded to concentrate the microbial fraction by filtering each through a 47 mm-diameter, 0.22 µm pore-size polycarbonate membrane with a peristaltic pump. The filters were flash-frozen in liquid nitrogen at sea and were transferred to -80°C storage in the lab.</p>
Specified by the Principal Investigator(s)
- Loaded CSV file "bcodmo_RC0078_hom_exp_sra_metadata.csv" using filename as resource name, with "nd" and empty strings treated as missing values
- Renamed field "year_month_day" to "Date"
- Renamed fields: Depth_meters to Depth, Latitude_N to Latitude, Longitude_E to Longitude, accession_number_url to accession_sra_url, accession_number_text to accession_number
- Output to "997408_v1_rc0078_hom_exp_sra_metadata.csv"
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
Illumina NovaSeq 6000
Illumina NovaSeq 6000
PI Supplied Instrument Name: Illumina NovaSeq 6000 PI Supplied Instrument Description:NCBI Description: Samples were DNase treated (RNase free). Library was prepared with Illumina's Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10 bp IDT for Illumina indices. Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
Sea-Bird SBE9 CTD profiler
Sea-Bird SBE9 CTD profiler
PI Supplied Instrument Name: Sea-Bird SBE9 CTD profiler PI Supplied Instrument Description:Sea-Bird SBE9 CTD profiler Instrument Name: CTD Sea-Bird SBE 911plus Instrument Short Name:CTD SBE 911plus Instrument Description: The Sea-Bird SBE 911 plus is a type of CTD instrument package for continuous measurement of conductivity, temperature and pressure. The SBE 911 plus includes the SBE 9plus Underwater Unit and the SBE 11plus Deck Unit (for real-time readout using conductive wire) for deployment from a vessel. The combination of the SBE 9 plus and SBE 11 plus is called a SBE 911 plus. The SBE 9 plus uses Sea-Bird's standard modular temperature and conductivity sensors (SBE 3 plus and SBE 4). The SBE 9 plus CTD can be configured with up to eight auxiliary sensors to measure other parameters including dissolved oxygen, pH, turbidity, fluorescence, light (PAR), light transmission, etc.). more information from Sea-Bird Electronics Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0058/
deck incubator
deck incubator
PI Supplied Instrument Name: deck incubator PI Supplied Instrument Description:Seawater was transferred to acid-clean, blue-tinted, 5-L polycarbonate carboys for acclimation in a deck incubator with flow-through surface seawater. Instrument Name: Shipboard Incubator Instrument Short Name: Instrument Description: A device mounted on a ship that holds water samples under conditions of controlled temperature or controlled temperature and illumination.
Cruise: RC0078
RC0078
R/V Rachel Carson (UW)
Community Standard Description
International Council for the Exploration of the Sea
R/V Rachel Carson (UW)
vessel
RC0078
Anitra E. Ingalls
University of Washington
R/V Rachel Carson (UW)
Community Standard Description
International Council for the Exploration of the Sea
R/V Rachel Carson (UW)
vessel