Table of Contents

• Coverage
• Dataset Description
  • Methods & Sampling
  • Data Processing Description
  • BCO-DMO Processing Description
• Related Publications
• Related Datasets
• Parameters
• Instruments
• Deployments
• Project Information
• Funding

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).

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).

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.

- 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".

NSF Award Abstract:
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.

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.

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.