Table of Contents

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

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 <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 <3 h were randomly selected for sequencing.

Genome assembly and draft annotation were performed by SCGC as described in the center’s webpage https://scgc.bigelow.org/capabilities/service-description/.

Raw reads of SAGs were processed as described in Zhao et al., ISME 2025. They are available in NCBI under BioProject number PRJNA1124867.

- 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".

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.