http://lod.bco-dmo.org/id/dataset/986605
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
2025-10-13
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Metagenome accession numbers for samples collected in the eastern tropical North Pacific Ocean in 2017 on R/V Oceanus cruise 1704A
2025-10-27
publication
2025-10-27
revision
BCO-DMO Linked Data URI
2025-10-27
creation
http://lod.bco-dmo.org/id/dataset/986605
John Michael Beman
University of California-Merced
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: Beman, J. M. (2025) Metagenome accession numbers for samples collected in the eastern tropical North Pacific Ocean in 2017 on R/V Oceanus cruise 1704A. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-10-27 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/986605 [access date]
OC1704A metagenome accession numbers Dataset Description: Methods and Sampling: <p>Water samples were collected for DNA extraction using sampling bottles deployed on the CTD rosette. At each depth, 2-liter (L) samples were filtered through 0.22-micrometer (µm) filters (Millipore, Darmstadt, Germany) using a peristaltic pump and frozen until extraction. DNA was extracted following Beman et al. (2012) and sent for metagenome sequencing in the Vincent J. Coates Genome Sequencing Laboratory (GSL) at the University of California, Berkeley. For each sample, 250 ng of genomic DNA was sheared and libraries were prepared using the KAPA HyperPrep Kit (Kapa Biosystems, Wilmington, MA, USA). Samples were pooled into a single lane and sequenced via 150- cycle paired-end sequencing on the Illumina HiSeq 4000 platform (Illumina, Inc., San Diego, CA, USA).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1555375 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1555375
onGoing
John Michael Beman
University of California-Merced
650-823-7925
5200 North Lake Road
Merced
CA
95343
USA
jmbeman@gmail.com
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Latitude
Longitude
Date
Station
Depth
Repository
Biosample_accession
Sequencing_technology
Illumina HiSeq 4000
theme
None, User defined
latitude
longitude
date
station
depth
sample description
NCBI BioProject accession
instrument
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
instrument
BCO-DMO Standard Instruments
OC1704A
service
Deployment Activity
San Diego, California to Mazatlan, Mexico
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.
CAREER: Oxygen sensitivity of aerobic respiration and nitrification in oxygen minimum zones and biogeochemical feedbacks to deoxygenation
https://bemanlab.org/about/research/research-etnp-and-goc/
CAREER: Oxygen sensitivity of aerobic respiration and nitrification in oxygen minimum zones and biogeochemical feedbacks to deoxygenation
<p><em>NSF Award Abstract:</em><br />
Aerobic microorganisms in the ocean help regulate biogeochemical nutrient cycles through the linked production and consumption of dissolved oxygen (DO) and organic matter. Concentrations of DO have been shown to be steadily decreasing in deeper ocean waters and the resulting areas of critically low DO content, known as oxygen minimum zones (OMZs), are expanding. While this phenomenon is recognized as having potentially serious impacts on biogeochemical cycles where OMZs are growing, surprisingly little research has been done to identify the mechanisms and quantify the specific processes that will affect these changes. This project will study the connection between changing DO concentrations and nutrient cycling in the interior of the ocean. The oxidation of nitrogen compounds (ammonia and nitrite in particular) is strongly influenced by DO concentrations. Because of the complex and connected nature of marine biogeochemical reactions that involve DO, each one potentially altered by concentration changes, this research is critical for a complete understanding of how ocean chemistry will change in the near future. The project will incorporate education into the research by developing materials to teach high school students about the nitrogen cycle, by developing a marine chemistry based course for undergraduates that will give them both field and computational experience, and by building on past efforts to include traditionally underrepresented groups in science. One of the graduate students funded by this project will translate lectures into Spanish and make these available on the internet for increased accessibility for minority students.</p>
<p>The world's largest oxygen minimum zone (OMZ), located in the Eastern Tropical North Pacific (ETNP), is an ideal study site for research into the effects of varying dissolved oxygen (DO) concentrations on nutrient cycling in the interior ocean. Throughout this OMZ, the extent of anoxia exhibits a range that allows for study of the effect of changing DO content on the rates and mechanisms that control consumption of DO and organic matter by aerobic microorganisms in a 'real world' setting. In particular, ammonia and nitrite oxidation, reactions that play a critical role in the nitrogen cycle, are likely to be significantly affected by varying DO concentration. This project will evaluate aerobic respiration, ammonia, and nitrite oxidation rates at various stations in the ETNP, examine carefully controlled incubations, and develop primers to target active microorganisms in the OMZ; all to quantify the connections between DO and these biogeochemical nutrient cycles. The research will also examine the hypothesis that more organic carbon is respired in waters with low DO and a shallow OMZ than previously thought and evaluate the possibility that nitrogen cycling in low DO regions could push OMZs to anoxia due to nitrite oxidation coupled with nitrate reduction, which could potentially accelerate DO consumption. With the expansion of OMZ's in a changing ocean, it is crucial to more fully understand the connections between these various, complex, components.</p>
RANDOM
largerWorkCitation
project
eng; USA
oceans
San Diego, California to Mazatlan, Mexico
-110
-106.5
16
20.5
2017-04-20
2017-04-27
Eastern Tropical North Pacific Ocean
0
BCO-DMO catalogue of parameters from Metagenome accession numbers for samples collected in the eastern tropical North Pacific Ocean in 2017 on R/V Oceanus cruise 1704A
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/988047.rdf
Name: Latitude
Units: degrees North
Description: <p>Sampling latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/988048.rdf
Name: Longitude
Units: degrees East
Description: <p>Sampling longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/988049.rdf
Name: Date
Units: unitless
Description: <p>Sampling date</p>
http://lod.bco-dmo.org/id/dataset-parameter/988050.rdf
Name: Station
Units: unitless
Description: <p>Station number</p>
http://lod.bco-dmo.org/id/dataset-parameter/988051.rdf
Name: Depth
Units: meters (m)
Description: <p>Sample depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/988052.rdf
Name: Repository
Units: unitless
Description: <p>Database name that contains the metagenome sequences</p>
http://lod.bco-dmo.org/id/dataset-parameter/988053.rdf
Name: Biosample_accession
Units: unitless
Description: <p>NCBI BioSample accession</p>
http://lod.bco-dmo.org/id/dataset-parameter/988054.rdf
Name: Sequencing_technology
Units: unitless
Description: <p>Instrument model</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/986605/data/download
download
onLine
dataset
<p>Water samples were collected for DNA extraction using sampling bottles deployed on the CTD rosette. At each depth, 2-liter (L) samples were filtered through 0.22-micrometer (µm) filters (Millipore, Darmstadt, Germany) using a peristaltic pump and frozen until extraction. DNA was extracted following Beman et al. (2012) and sent for metagenome sequencing in the Vincent J. Coates Genome Sequencing Laboratory (GSL) at the University of California, Berkeley. For each sample, 250 ng of genomic DNA was sheared and libraries were prepared using the KAPA HyperPrep Kit (Kapa Biosystems, Wilmington, MA, USA). Samples were pooled into a single lane and sequenced via 150- cycle paired-end sequencing on the Illumina HiSeq 4000 platform (Illumina, Inc., San Diego, CA, USA).</p>
Specified by the Principal Investigator(s)
- Imported original file "BCODMO_BEMAN_ETNP17_Metagenomes.xlsx" into the BCO-DMO system.
- Converted date format to YYYY-MM-DD.
- Renamed fields to comply with BCO-DMO naming conventions.
- Saved the final file as "986605_v1_oc1704a_metagenome_accession_numbers.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 HiSeq 4000
Illumina HiSeq 4000
PI Supplied Instrument Name: Illumina HiSeq 4000 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.
Cruise: OC1704A
OC1704A
R/V Oceanus
Community Standard Description
International Council for the Exploration of the Sea
R/V Oceanus
vessel
OC1704A
John Michael Beman
R/V Oceanus
Community Standard Description
International Council for the Exploration of the Sea
R/V Oceanus
vessel