http://lod.bco-dmo.org/id/dataset/998771
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
2026-05-18
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Metagenome from the Pacific Ocean OMZ from the SAR11 in OMZs project
2026-05-18
publication
2026-05-18
revision
BCO-DMO Linked Data URI
2026-05-18
creation
http://lod.bco-dmo.org/id/dataset/998771
Kostas Konstantinidis
Georgia Institute of Technology
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: Konstantinidis, K. (2026) Metagenome from the Pacific Ocean OMZ. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-05-18 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/998771 [access date]
Metagenome from the Pacific Ocean OMZ Dataset Description: Methods and Sampling: <p>Samples for metagenomic sequencing were collected from the Eastern Tropical North Pacific (ETNP) Oxygen Minimum Zone (OMZ) on R/V Sally Ride (SR2114) from December 2021 to January 2022. Sea water for metagenomes was collected from all nine depths for all five sampling stations. Collections were made using Niskin bottles on a rosette containing a conductivity–temperature–depth profiler (Sea-Bird SBE 911plus), as described in Tsementzi et al., 2016.</p>
<p>DNA was extracted from biomass on collecting filters using the MoBio Power Soil kit (MoBio Inc. Carlsbad, CA, USA) and libraries were prepared for metagenomic sequencing using the Illumina DNA library prep kit with unique dual indexing according to manufacturer's instructions, except that the protocol was terminated after isolation of cleaned double stranded libraries. An equimolar mixture of the libraries was 2 sequenced on an Illumina NovaSeq 6000 instrument at the Molecular Evolution Core, Georgia Institute of Technology.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2129823 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2129823
onGoing
Kostas Konstantinidis
Georgia Institute of Technology
404-385-3628
Mason Building 790 Atlantic Drive
Atlanta
GA
30332
USA
kostas@ce.gatech.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Sample_ID
DNA_Concentration
Date_Sampled
Date_Extracted
Latitude
Longitude
Depth
Volume_Filtered
Station
Oxygen_Concentration
Experiment_Accession
Instrument
Study_Accession
Sample_Accession
Bioproejct_number
Total_Bases
Library_Name
Illumina NovaSeq 6000
Niskin bottles
theme
None, User defined
sample identification
genetic material concentration
date
latitude
longitude
depth
volume of water filtered
station
dissolved Oxygen
NCBI SRA experiment accession (SRX)
instrument
NCBI SRA study accession (SRP)
NCBI SRA Sample accession (SRS)
NCBI BioProject accession
count
sample description
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Niskin bottle
instrument
BCO-DMO Standard Instruments
SR2114
service
Deployment Activity
Eastern Tropical Pacific from Costa Rica to San Diego, CA, USA
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: Microdiversity drives ecosystem function: SAR11 bacteria as models for oceanic nitrogen loss
https://osprey.bco-dmo.org/project/885604
Collaborative Research: Microdiversity drives ecosystem function: SAR11 bacteria as models for oceanic nitrogen loss
<p><em>NSF Award Abstract:</em><br />
This project studies how low oxygen availability influences the biodiversity and ecological role of SAR11 bacteria, one of the most abundant microbial groups in the ocean. The work involves oceanographic sampling across a range of oxygen and nutrient levels in the Eastern Tropical North Pacific Ocean. Using a combination of genomic, microbiological, and biogeochemical methods, the study identifies the mechanisms by which SAR11 strains diversify into separate niches and species and contribute biochemically to the ecosystem, likely through removing nitrogen from seawater. The project equips the next generation of researchers and educators, notably those from underrepresented minority groups, to use oceanographic, genomic, and microbiological concepts to meet contemporary scientific challenges. This goal is met through a combination of bioinformatic workshops that target undergraduate students from the University System of Puerto Rico, middle school teacher-training workshops, and middle or high school teacher internships in the investigator’s labs. This multifaceted research and educational agenda fills a gap in our understanding of marine biological diversity, identifies the contribution of SAR11 bacteria to nutrient and carbon cycles in low oxygen oceans, and provides lessons and analytical tools to study microbial processes in other ecosystems.</p>
<p>This project has two aims. Aim 1 employs comparative metagenomic and single-cell genomic analyses to identify metabolic properties that distinguish SAR11 clades from low oxygen regions and processes of selection or gene flow operating across the clades. Aim 2 combines microbial transcriptomics, incubation experiments with isotope tracers, and culturing to delimit the oxygen and nutrient conditions that define the niche space of each SAR11 clade and to correlate SAR11 gene transcription with community biochemical outcomes, including nitrogen loss through denitrification. The results of these aims and the informatic methods used to probe microbial microdiversity are disseminated through genomics-focused undergraduate workshops, and new teacher-training educational modules, including lab-based modules focused on the importance of microorganisms under environmental change in the oceans. Data, manuscripts, and informatics workflows from this project are made publicly available. The results are critical for resolving the processes that create and sustain microbial diversity in the oceans and informing biogeochemical models that predict how diversity influences ecosystem processes.</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>
SAR11 in OMZs
largerWorkCitation
project
eng; USA
oceans
Eastern Tropical Pacific from Costa Rica to San Diego, CA, USA
-107.7
-90.4497
11.8122
16.9798
2021-12-30
2022-10-16
Eastern Tropical North Pacific, off Colima, Mexico
0
BCO-DMO catalogue of parameters from Metagenome from the Pacific Ocean OMZ from the SAR11 in OMZs 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
http://lod.bco-dmo.org/id/dataset-parameter/998802.rdf
Name: Sample_ID
Units: unitless
Description: <p>Sample ID number</p>
http://lod.bco-dmo.org/id/dataset-parameter/998803.rdf
Name: DNA_Concentration
Units: micromoles per liter
Description: <p>DNA concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/998804.rdf
Name: Date_Sampled
Units: unitless
Description: <p>Date sampled</p>
http://lod.bco-dmo.org/id/dataset-parameter/998805.rdf
Name: Date_Extracted
Units: unitless
Description: <p>Date of DNA extraction</p>
http://lod.bco-dmo.org/id/dataset-parameter/998806.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Latitude where sample was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/998808.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Longitude where sample was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/998810.rdf
Name: Depth
Units: meters (m)
Description: <p>Depth of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/998812.rdf
Name: Volume_Filtered
Units: milliliters (mL)
Description: <p>Volume of water filtered</p>
http://lod.bco-dmo.org/id/dataset-parameter/998813.rdf
Name: Station
Units: unitless
Description: <p>Station number</p>
http://lod.bco-dmo.org/id/dataset-parameter/998814.rdf
Name: Oxygen_Concentration
Units: micromoles per kilogram
Description: <p>Oxygen concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/998815.rdf
Name: Experiment_Accession
Units: unitless
Description: <p>NCBI experiment accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/998816.rdf
Name: Instrument
Units: unitless
Description: <p>Instrument used in sequencing</p>
http://lod.bco-dmo.org/id/dataset-parameter/998817.rdf
Name: Study_Accession
Units: unitless
Description: <p>NCBI study accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/998818.rdf
Name: Sample_Accession
Units: unitless
Description: <p>NCBI sample accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/998819.rdf
Name: Bioproejct_number
Units: unitless
Description: <p>NCBI BioProject number</p>
http://lod.bco-dmo.org/id/dataset-parameter/998820.rdf
Name: Total_Bases
Units: number of bases
Description: <p>Total number of bases</p>
http://lod.bco-dmo.org/id/dataset-parameter/998821.rdf
Name: Library_Name
Units: Matches Sample ID above plus another unique identifier.
Description: <p>ID of the sequenced library</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/998771/data/download
download
onLine
dataset
<p>Samples for metagenomic sequencing were collected from the Eastern Tropical North Pacific (ETNP) Oxygen Minimum Zone (OMZ) on R/V Sally Ride (SR2114) from December 2021 to January 2022. Sea water for metagenomes was collected from all nine depths for all five sampling stations. Collections were made using Niskin bottles on a rosette containing a conductivity–temperature–depth profiler (Sea-Bird SBE 911plus), as described in Tsementzi et al., 2016.</p>
<p>DNA was extracted from biomass on collecting filters using the MoBio Power Soil kit (MoBio Inc. Carlsbad, CA, USA) and libraries were prepared for metagenomic sequencing using the Illumina DNA library prep kit with unique dual indexing according to manufacturer's instructions, except that the protocol was terminated after isolation of cleaned double stranded libraries. An equimolar mixture of the libraries was 2 sequenced on an Illumina NovaSeq 6000 instrument at the Molecular Evolution Core, Georgia Institute of Technology.</p>
Specified by the Principal Investigator(s)
<p>The raw shotgun metagenomes are provided, and are available in NCBI under BioProject number PRJNA1124864.</p>
Specified by the Principal Investigator(s)
- Imported original Excel file "Table S2. Sample information for the metagenomes from the ETNP OMZ.xlsx" (sheet 1) into the BCO-DMO data processing system.
- Converted "Date Sampled" from format "%m-%d-%y" to "%Y-%m-%d".
- Converted "Date Extracted" from format "%m.%d.%y" to "%Y-%m-%d".
- Converted "Lat N" from degrees-decimal_minutes format to decimal degrees using directional N, and renamed the new column "Latitude".
- Converted "Long W" from degrees-decimal_minutes format to decimal degrees using directional W, and renamed the new column "Longitude".
- Rounded Latitude and Longitude to maximum 4 decimal places.
- Renamed columns to comply with BCO-DMO naming conventions.
- Saved the final file as "998771_v1_etnp_metagenomes_zhao.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:Libraries were sequenced on an Illumina NovaSeq 6000 instrument at the Molecular Evolution Core, Georgia Institute of Technology. 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.
Niskin bottles
Niskin bottles
PI Supplied Instrument Name: Niskin bottles PI Supplied Instrument Description:Niskin bottles on a rosette were used to collect the water samples. 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: SR2114
SR2114
R/V Sally Ride
Community Standard Description
International Council for the Exploration of the Sea
R/V Sally Ride
vessel
SR2114
Mark A. Altabet
University of Massachusetts Dartmouth
R/V Sally Ride
Community Standard Description
International Council for the Exploration of the Sea
R/V Sally Ride
vessel