http://lod.bco-dmo.org/id/dataset/998887
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
2026-05-19
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
SAGs from the Pacific Ocean OMZ from the SAR11 in OMZs project
2026-05-19
publication
2026-05-19
revision
BCO-DMO Linked Data URI
2026-05-19
creation
http://lod.bco-dmo.org/id/dataset/998887
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) SAGs from the Pacific Ocean OMZ. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-05-19 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/998887 [access date]
SAGs from the Pacific Ocean OMZ Dataset Description: Methods and Sampling: <p>Water samples were collected using Niskin bottles on a rosette containing a conductivity–temperature–depth profiler (Sea-Bird SBE 911plus). The water was prepared by cryopreservation according to the protocol recommended by the Bigelow Single Cell Genomics Center (SCGC). Sorting was performed on 4 April 2023 (within &lt;2 months from the date the first sample was collected) and SAGs were generated with the modified genomic DNA amplification technique, WGA-Y, which enables a substantially improved average genome recovery from single cells (service S-202). In total, 105 SAGs with Cp values &lt;3 h were randomly selected for sequencing.</p>
<p>Genome assembly and draft annotation were performed by SCGC as described in the center’s webpage <a href="https://scgc.bigelow.org/capabilities/service-description/" target="_blank">https://scgc.bigelow.org/capabilities/service-description/</a>.</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
SAG_identifier
Station
Latitude
Longitude
Depth
Genome
Clade
Completeness
Contamination
Strain_heterogeneity
Experiment_Accession
Study_Accession
Sample_Accession
SAG_ID
Illumina NextSeq 500
Sea-Bird SBE 911plus
Niskin bottles
theme
None, User defined
sample identification
station
latitude
longitude
depth
sample description
NCBI SRA experiment accession (SRX)
NCBI SRA study accession (SRP)
NCBI SRA Sample accession (SRS)
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
CTD Sea-Bird SBE 911plus
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: 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
-106.2833
-104.9
18.1667
18.8833
2026-05-19
Eastern Tropical North Pacific, off Colima, Mexico
0
BCO-DMO catalogue of parameters from SAGs 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/998914.rdf
Name: SAG_identifier
Units: unitless
Description: <p>SAG identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/998915.rdf
Name: Station
Units: unitless
Description: <p>Station number</p>
http://lod.bco-dmo.org/id/dataset-parameter/998916.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Latitude of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/998918.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Longitude of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/998920.rdf
Name: Depth
Units: meters (m)
Description: <p>Depth of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/998922.rdf
Name: Genome
Units: unitless
Description: <p>ID of the SAG sequenced</p>
http://lod.bco-dmo.org/id/dataset-parameter/998923.rdf
Name: Clade
Units: unitless
Description: <p>Clade designation according to the concatenated gene tree shown in Figure 1 of Zhao et al., ISME J</p>
http://lod.bco-dmo.org/id/dataset-parameter/998924.rdf
Name: Completeness
Units: ranging from 0 to 100%
Description: <p>Genome quality was assessed using CheckM v1.5.3</p>
http://lod.bco-dmo.org/id/dataset-parameter/998925.rdf
Name: Contamination
Units: ranging from 0 to 100%
Description: <p>Genome quality was assessed using CheckM v1.5.3</p>
http://lod.bco-dmo.org/id/dataset-parameter/998926.rdf
Name: Strain_heterogeneity
Units: ranging from 0 to 100%
Description: <p>Genome quality was assessed using CheckM v1.5.3</p>
http://lod.bco-dmo.org/id/dataset-parameter/998927.rdf
Name: Experiment_Accession
Units: unitless
Description: <p>NCBI experiment accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/998928.rdf
Name: Study_Accession
Units: unitless
Description: <p>NCBI study accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/998929.rdf
Name: Sample_Accession
Units: unitless
Description: <p>NCBI sample accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/998930.rdf
Name: SAG_ID
Units: unitless
Description: <p>ID of the SAG sequenced (same as Genome above but with hyphens included)</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/998887/data/download
download
onLine
dataset
<p>Water samples were collected using Niskin bottles on a rosette containing a conductivity–temperature–depth profiler (Sea-Bird SBE 911plus). The water was prepared by cryopreservation according to the protocol recommended by the Bigelow Single Cell Genomics Center (SCGC). Sorting was performed on 4 April 2023 (within &lt;2 months from the date the first sample was collected) and SAGs were generated with the modified genomic DNA amplification technique, WGA-Y, which enables a substantially improved average genome recovery from single cells (service S-202). In total, 105 SAGs with Cp values &lt;3 h were randomly selected for sequencing.</p>
<p>Genome assembly and draft annotation were performed by SCGC as described in the center’s webpage <a href="https://scgc.bigelow.org/capabilities/service-description/" target="_blank">https://scgc.bigelow.org/capabilities/service-description/</a>.</p>
Specified by the Principal Investigator(s)
<p>Raw reads of SAGs were processed as described in Zhao et al., ISME 2025. They are available in NCBI under BioProject number PRJNA1124867.</p>
Specified by the Principal Investigator(s)
- Imported original file "Table S1. Sample information for the SAGs from the ETNP OMZ.xlsx" (sheet 1) twice: once with header row 106 as a lookup table named "station_list", and once with header row 2 as the main data table.
- Filtered the main data file to keep only rows where ROW_NUMBER < 103.
- Joined "station_list" to the main data file in half-outer mode, matching on the SAG ID number, bringing in columns Depth, Latitude, Longitude, SAG identifier, and Station.
- Renamed columns to comply with BCO-DMO naming conventions.
- Converted Latitude from degrees-decimal_minutes format (North) to decimal degrees.
- Converted Longitude from degrees-decimal_minutes format (West) to decimal degrees
- Rounded Latitude and Longitude to maximum 4 decimal places.
- Saved the final file as "998887_v1_sags_pacific_omz.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 NextSeq 500
Illumina NextSeq 500
PI Supplied Instrument Name: Illumina NextSeq 500 PI Supplied Instrument Description:SAG paired-end libraries were created with Nextera XT kits (Illumina), sequenced with a NextSeq 500 (Illumina) available at the Bigelow Center. 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 SBE 911plus
Sea-Bird SBE 911plus
PI Supplied Instrument Name: Sea-Bird SBE 911plus PI Supplied Instrument Description:Water samples were collected using Niskin bottles on a rosette containing a conductivity–temperature–depth profiler (Sea-Bird SBE 911plus). 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/
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/