http://lod.bco-dmo.org/id/dataset/998957
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)
Sample information for the metagenomes from the Gulf of Mexico collected on R/V Endeavor cruise EN509 in May 2012
2026-05-20
publication
2026-05-20
revision
BCO-DMO Linked Data URI
2026-05-20
creation
http://lod.bco-dmo.org/id/dataset/998957
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) Sample information for the metagenomes from the Gulf of Mexico collected on R/V Endeavor cruise EN509 in May 2012. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-05-20 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/998957 [access date]
Metagenome from Gulf of Mexico Dataset Description: Methods and Sampling: <p>Water column samples were collected during CTD casts from the May 2012 R/V Endeavour cruise EN509 and shotgun metagenomes were sequenced from the surface (~3 meters (m), the mixed layer (ML; 15-25m), the deep chlorophyll maximum (DCM; 70-90m), below the DCM but above the oxygen minimum zone (OMZ; 100-150m), and the OMZ (200-400m) from three stations (2, 5, and 8) in the northwest GoM (Fig. 1A of Conrad et al., 2026).</p>
<p>Four additional metagenomes were sequenced from below the OMZ (Deep; 600, 1000, 1470 and 2107m) from station 5. Station 2 was near the edge of the Texas-Louisiana Shelf about 50 miles southeast from the mouth of the Mississippi river. Station 8 and 5 were over the TX-LA Slope about 190 and 270 mi. southeast of Galveston, TX with station 8 nearer the TX-LA Shelf and station 5 nearer the edge of the TX-LA slope. Fluorescence, oxygen, salinity, and temperature measurements were similar at all stations except salinity was lower (29.6 vs. 36 PSU) and fluorescence was increased (0.9 vs. 0.07 milligrams per cubic meter (mg/m³) at the surface of station 2 while the fluorescence peak of the DCM layer was reduced (0.3 vs. 0.8 mg/m³) compared to stations 5 and 8 (Fig. 1B, C, D, and E of Conrad et al., 2026). Temperature and salinity were most similar for all samples from the ML and DCM while salinity was variable across surface samples and temperature and salinity were variable across aOMZ and OMZ samples (Fig. 1E of Conrad et al., 2026).</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
Acession
Sample_Name
Vessel
Cruise
Ocean
Date
Year
Month
Day
Station
Lat
Lon
Description
Depth
Temp
Salinity
Density
Fluoresence
Oxygen
Xmiss
Conductivity
Par
Mean_PO4
Mean_Si
Mean_NO3_NO2
Mean_N_star
Sequencing_Effort_Gb
Sequencing_Effort_Bp
Metagenome_Reads_GC
Average_Genome_Size
Nonpareil_Diversity
Diversity_Covered
Contigs_Assembled
Assembled_Length
Assembled_N50
Assembled_GC
Predicted_CDS
Reads_Mapping_to_Assembly
Reads_Mapping_to_rMAGs
Sea-Bird SBE 911plus
Niskin bottles
theme
None, User defined
NCBI SRA experiment accession (SRX)
sample identification
ship
Cruise identifier
ocean
date
year
month of year
day of month
station
latitude
longitude
sample description
depth
water temperature at measurement depth
salinity
density
fluorescence
dissolved Oxygen
transmission
conductivity
PAR
phosphate
Silicon
nitrate plus nitrite
No BCO-DMO term
count
length
featureType
BCO-DMO Standard Parameters
CTD Sea-Bird SBE 911plus
Niskin bottle
instrument
BCO-DMO Standard Instruments
EN509
service
Deployment Activity
Gulf of 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.
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
Gulf of Mexico
-92.701
-88.4893
26.095
28.8505
2012-05-26
2012-06-02
Eastern Tropical North Pacific, off Colima, Mexico
0
BCO-DMO catalogue of parameters from Sample information for the metagenomes from the Gulf of Mexico collected on R/V Endeavor cruise EN509 in May 2012
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/999064.rdf
Name: Acession
Units: unitless
Description: <p>NCBI experiment accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/999065.rdf
Name: Sample_Name
Units: unitless
Description: <p>Sample ID number</p>
http://lod.bco-dmo.org/id/dataset-parameter/999066.rdf
Name: Vessel
Units: unitless
Description: <p>Ship name</p>
http://lod.bco-dmo.org/id/dataset-parameter/999067.rdf
Name: Cruise
Units: unitless
Description: <p>Cruise ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/999068.rdf
Name: Ocean
Units: unitless
Description: <p>Ocean where samples were collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/999069.rdf
Name: Date
Units: unitless
Description: <p>Date</p>
http://lod.bco-dmo.org/id/dataset-parameter/999070.rdf
Name: Year
Units: unitless
Description: <p>4-digit year</p>
http://lod.bco-dmo.org/id/dataset-parameter/999071.rdf
Name: Month
Units: unitless
Description: <p>Month</p>
http://lod.bco-dmo.org/id/dataset-parameter/999072.rdf
Name: Day
Units: unitless
Description: <p>Day of month</p>
http://lod.bco-dmo.org/id/dataset-parameter/999073.rdf
Name: Station
Units: unitless
Description: <p>Station number</p>
http://lod.bco-dmo.org/id/dataset-parameter/999074.rdf
Name: Lat
Units: decimal degrees
Description: <p>Latitude of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/999076.rdf
Name: Lon
Units: decimal degrees
Description: <p>Longitude of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/999078.rdf
Name: Description
Units: unitless
Description: <p>Sample description: SURFACE =Surface (3m); ML = mixed layer (15–25 m); DCM = Deep Chlorophyll Maximum (70–90 m); aOMZ = below the DCM but above the oxygen minimum (OM) depth (100–150 m); OMZ = oxygen minimum zone depth (100–150 m); DEEP = below the OM depth (600, 1,000, 1,470, or 2,107 m)</p>
http://lod.bco-dmo.org/id/dataset-parameter/999079.rdf
Name: Depth
Units: meters (m)
Description: <p>Sample depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/999081.rdf
Name: Temp
Units: degrees Celsius
Description: <p>Water temperature</p>
http://lod.bco-dmo.org/id/dataset-parameter/999082.rdf
Name: Salinity
Units: PSU
Description: <p>Water sailinity</p>
http://lod.bco-dmo.org/id/dataset-parameter/999083.rdf
Name: Density
Units: sigma theta
Description: <p>Density</p>
http://lod.bco-dmo.org/id/dataset-parameter/999084.rdf
Name: Fluoresence
Units: milligrams per cubic meter (mg/m^3)
Description: <p>Fluorescence</p>
http://lod.bco-dmo.org/id/dataset-parameter/999085.rdf
Name: Oxygen
Units: micromolar (uM)
Description: <p>Oxygen concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/999086.rdf
Name: Xmiss
Units: ranging 0-100%.
Description: <p>percent of total</p>
http://lod.bco-dmo.org/id/dataset-parameter/999087.rdf
Name: Conductivity
Units: Siemens per meter (S/m)
Description: <p>Conductivity</p>
http://lod.bco-dmo.org/id/dataset-parameter/999088.rdf
Name: Par
Units: micromoles of photons per square meter per second (μmol*m^-2*s^-1)
Description: <p>Photosynthetically active radiation</p>
http://lod.bco-dmo.org/id/dataset-parameter/999089.rdf
Name: Mean_PO4
Units: micromolar (uM)
Description: <p>Mean phosphate concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/999090.rdf
Name: Mean_Si
Units: micromolar (uM)
Description: <p>Mean silicon concetration</p>
http://lod.bco-dmo.org/id/dataset-parameter/999091.rdf
Name: Mean_NO3_NO2
Units: micromolar (uM)
Description: <p>Mean nitrate + nitrite</p>
http://lod.bco-dmo.org/id/dataset-parameter/999092.rdf
Name: Mean_N_star
Units: unknown
Description: <p>(description needed)</p>
http://lod.bco-dmo.org/id/dataset-parameter/999093.rdf
Name: Sequencing_Effort_Gb
Units: Giga-basepairs (Gb)
Description: <p>Total sequencing performed</p>
http://lod.bco-dmo.org/id/dataset-parameter/999094.rdf
Name: Sequencing_Effort_Bp
Units: Basepairs (Bp)
Description: <p>Total sequencing performed</p>
http://lod.bco-dmo.org/id/dataset-parameter/999095.rdf
Name: Metagenome_Reads_GC
Units: ranging 25-75%, typically
Description: <p>average G+C% of metagenomics reads</p>
http://lod.bco-dmo.org/id/dataset-parameter/999096.rdf
Name: Average_Genome_Size
Units: Mega-basepairs (Mb)
Description: <p>Average Genome Size of sequences community</p>
http://lod.bco-dmo.org/id/dataset-parameter/999097.rdf
Name: Nonpareil_Diversity
Units: ranging 1-30, typically
Description: <p>Community diversity as estimated by Nonpareil v3.401</p>
http://lod.bco-dmo.org/id/dataset-parameter/999098.rdf
Name: Diversity_Covered
Units: ranging 0-100%.
Description: <p>% of community diversity recovered by sequencing based on Nonpareil v3.401</p>
http://lod.bco-dmo.org/id/dataset-parameter/999099.rdf
Name: Contigs_Assembled
Units: integer, number
Description: <p>Number of large contigs assembled</p>
http://lod.bco-dmo.org/id/dataset-parameter/999100.rdf
Name: Assembled_Length
Units: Basepairs (Bp)
Description: <p>total length of assembled contigs</p>
http://lod.bco-dmo.org/id/dataset-parameter/999101.rdf
Name: Assembled_N50
Units: Basepairs (Bp)
Description: <p>The length of the shortest contig that covers at least 50% of the total assembly</p>
http://lod.bco-dmo.org/id/dataset-parameter/999102.rdf
Name: Assembled_GC
Units: ranging 25-75%, typically
Description: <p>average G+C% of contigs</p>
http://lod.bco-dmo.org/id/dataset-parameter/999103.rdf
Name: Predicted_CDS
Units: integer, number
Description: <p>number of predicted proteins-coding genes of the assembly</p>
http://lod.bco-dmo.org/id/dataset-parameter/999104.rdf
Name: Reads_Mapping_to_Assembly
Units: ranging 0-100%.
Description: <p>percent of total reads mapping back to the assembly.</p>
http://lod.bco-dmo.org/id/dataset-parameter/999105.rdf
Name: Reads_Mapping_to_rMAGs
Units: ranging 0-100%.
Description: <p>percent of total reads mapping back to the representative MAGs</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/998957/data/download
download
onLine
dataset
<p>Water column samples were collected during CTD casts from the May 2012 R/V Endeavour cruise EN509 and shotgun metagenomes were sequenced from the surface (~3 meters (m), the mixed layer (ML; 15-25m), the deep chlorophyll maximum (DCM; 70-90m), below the DCM but above the oxygen minimum zone (OMZ; 100-150m), and the OMZ (200-400m) from three stations (2, 5, and 8) in the northwest GoM (Fig. 1A of Conrad et al., 2026).</p>
<p>Four additional metagenomes were sequenced from below the OMZ (Deep; 600, 1000, 1470 and 2107m) from station 5. Station 2 was near the edge of the Texas-Louisiana Shelf about 50 miles southeast from the mouth of the Mississippi river. Station 8 and 5 were over the TX-LA Slope about 190 and 270 mi. southeast of Galveston, TX with station 8 nearer the TX-LA Shelf and station 5 nearer the edge of the TX-LA slope. Fluorescence, oxygen, salinity, and temperature measurements were similar at all stations except salinity was lower (29.6 vs. 36 PSU) and fluorescence was increased (0.9 vs. 0.07 milligrams per cubic meter (mg/m³) at the surface of station 2 while the fluorescence peak of the DCM layer was reduced (0.3 vs. 0.8 mg/m³) compared to stations 5 and 8 (Fig. 1B, C, D, and E of Conrad et al., 2026). Temperature and salinity were most similar for all samples from the ML and DCM while salinity was variable across surface samples and temperature and salinity were variable across aOMZ and OMZ samples (Fig. 1E of Conrad et al., 2026).</p>
Specified by the Principal Investigator(s)
<p>DNA was purifiedusing the Ampure XP-Beads (Beckman Coulter). DNA sequencing was performed using a Nextera XT DNA Sample Prep kit, and a paired-end strategy on an Illumina MiSeq sequencer available at the Molecular Core of Georgia Tech. Sequences are available in the National Center for Biotechnology Information (NCBI) under BioProject number PRJNA291283.</p>
Specified by the Principal Investigator(s)
- Imported sheet 1 of the original file named, "Supplemental_File_01-metaGs-revised.xlsx into table "998957_v1_metagenome_gom" into the BCO-DMO system.
- Filtered rows to keep only the first 19 rows, excluding secondary tables located on the data sheet.
- Combined Year (format Y), Month (format %B), and Day (format %d) columns into a new Date column formatted as %Y-%m-%d with type date.
- Renamed all columns to comply with BCO-DMO naming conventions.
- Saved the final file as "998957_v1_metagenome_gom.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
Sea-Bird SBE 911plus
Sea-Bird SBE 911plus
PI Supplied Instrument Name: Sea-Bird SBE 911plus PI Supplied Instrument Description:Collections were made 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:Collections were made using Niskin bottles on a rosette. 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: EN509
EN509
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel
EN509
Joseph Montoya
Georgia Institute of Technology
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel