Table of Contents

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

Other Grants:
* "National Science Foundation Graduate Research Fellowship Program" (Grant ID 1842402, National Science Foundation)
* "NOAA Margaret A. Davidson Fellowship" (Grant ID NA20NOS4200123, National Oceanic and Atmospheric Administration)

Methods and sampling are reported in Tucker et al., (2021)

Sample collection and environmental parameters

Between August 2017 and June 2019, seawater was collected from a depth of 2 m at 10 sites in and around Kāneʻohe Bay, Oʻahu, Hawaiʻi, on a near-monthly basis (20 sampling events over 23 months). At each station, seawater samples for biogeochemical analyses and nucleic acids were collected, and in situ measurements of seawater temperature, pH, and salinity were made with a YSI 6,600 sonde (YSI Incorporated, Yellow Springs, OH, USA). Approximately one L of seawater was prefiltered using an 85 μm Nitex mesh and subsequently collected on a 25-mm diameter 0.1-μm pore-sized polyethersulfone (PES) membrane for nucleic acids (Supor-100, Pall Gelman Inc., Ann Arbor, MI, USA). The filters were submerged in DNA lysis buffer (Suzuki et al., 2001; Yeo et al., 2013) and stored at −80 °C until extraction.

Subsamples for chlorophyll a were collected by filtering 125 mL of seawater onto 25-mm diameter GF/F glass microfiber filters (Whatman, GE Healthcare Life Sciences, Chicago, IL, USA), and stored in aluminum foil at −80 °C until extraction in 100% acetone and subsequent measurement of fluorescence with a Turner 10AU fluorometer (Turner Designs, Sunnyvale, CA, USA) followed standard techniques (Welschmeyer, 1994). Seawater for cellular enumeration was preserved in two-mL aliquots in a final concentration of 0.95% (v:v) paraformaldehyde (Electron Microscopy Services, Hatfield, PA, USA) at −80 °C until analyzed via flow cytometry. Cellular enumeration of cyanobacterial picophytoplankton (marine Synechococcus and Prochlorococcus), eukaryotic picophytoplankton, and non-cyanobacterial (presumably heterotrophic) bacteria and archaea (hereafter referred to as heterotrophic bacteria) was performed on an EPICS ALTRA flow cytometer (Beckman Coulter Inc., Brea, CA, USA), following the method of Monger and Landry (Monger & Landry, 1993).

DNA extraction and sequencing

Genomic DNA was extracted using a Qiagen Blood and Tissue Kit (Qiagen Inc., Valencia, CA, USA) with modifications (Becker, Brandon & Rappé, 2007). For each sample, 16S rRNA gene fragments were amplified by polymerase chain reaction using a dual-index sequencing strategy where barcoded universal primers 515-Y-F and 926R (Parada, Needham & Fuhrman, 2016) are complete with Illumina sequencing adapters, barcode, and index. The 25 µL reactions included 13 µL H2O, 0.5 µL each of forward and reverse primer at 0.2 µm final concentration, one µL gDNA (0.5 ng), and 10 µL 1 × 5PRIME Hot Master Mix (0.5 U Taq DNA polymerase, 45 mm KCl, 2.5 mm Mg2+, 200 μm dNTPs) (Quantabio, Beverly, MA, USA). PCR conditions included an initial denaturation at 95 °C for 2 min followed by 30 cycles of 95 °C for 45 s, 50 °C for 45 s, and 68 °C for 90 s, and a final 5 min extension at 68 °C. PCR products were inspected on a 1.5% agarose gel and quantified using the Qubit dsDNA HS Kit (Qubit 2.0, Life Technologies, Foster City, CA, USA). PCR products were normalized to 240 ng each, pooled, and purified using the QIAquick PCR Purification Kit (Qiagen, Hilden, Germany). Pooled libraries were then sequenced on an Illumina MiSeq v2 250 bp paired-end run at the Oregon State University Center for Genome Research & Biocomputing.

* No data value NA set to blank
* Split latitude and longitude value into own column.

In the upper water column of Earth's coastal and open oceans, roughly one million microscopic, single-celled bacteria inhabit each milliliter of seawater, where they play important roles in driving nutrient cycles and other processes that are vital to the habitability of these systems to other marine life. While some marine bacteria are similar to plants in that they use energy from the sun to transform the greenhouse gas carbon dioxide into living material and produce oxygen as a byproduct, other marine bacteria known as chemoheterotrophs are similar to humans and other animals in that they consume organic matter and oxygen, producing carbon dioxide as a consequence of their growth. Although they are limited in size and shape when observed under a microscope, genetic techniques such as DNA sequencing have revealed tremendous functional (i.e. what they are doing) and phylogenetic (i.e. how they are related) biodiversity in natural communities of marine bacteria. Despite this high genetic diversity, a single group of phylogenetically related chemoheterotrophic bacteria known as SAR11 can sometimes make up over 50% of the microscopic cells inhabiting seawater systems around the globe; it is considered one of the most abundant organisms on Earth and thus an important aspect of ocean ecology. While it is known that the SAR11 group consists of many distinct "types" that differ in abundance with location, depth and time, we know little about what genetically encoded features distinguish the different types, or how genetic characteristics are gained and lost within the group. The goal of this study is to use a genomics approach to understand the evolutionary processes that shape one of the most abundant groups of organisms on our planet, and to improve our theoretical understanding of the evolutionary processes that shape natural microbial biodiversity in general. This project will provide advanced, cross-disciplinary professional training for a postdoctoral scientist and a graduate student, and will increase the participation of underrepresented groups in scientific research by mentoring undergraduate students of native Hawaiian or Pacific Island ancestry in hands-on research and training. Results will be incorporated into a new university course offering on comparative genomics and microbial evolution. A culture collection of marine microorganisms will also be expanded and maintained, providing a valuable resource for other marine scientists.

This project will take advantage of recent advances in DNA sequencing technology and a high throughput extinction culturing approach in order to investigate the evolutionary characteristics of genomes from sympatric populations of the globally important SAR11 marine bacterial lineage. The major objectives of this project are to understand the forces that shape genomic diversity in large bacterial populations such as SAR11, and to determine the nature by which this diversity is reflected in functional differences between populations, as inferred from genomics. SAR11 cells will be isolated from similar ecosystems in the tropical North and South Pacific, as well as the coastal ocean of the subpolar North Pacific, in order to investigate the effect of geographic distance versus habitat similarity on the population genetics of free-living, planktonic marine bacteria. By opening a unique genomic window that encompasses SAR11 lineages of varying degrees of genetic divergence simultaneously, this study will facilitate the investigation of evolutionary dynamics that spans a continuum between macro- and microevolutionary processes. Quantitative information regarding the mechanisms by which genetic diversity is generated, propagated, and removed from native SAR11 populations will also help efforts to model the fate of SAR11 and other large marine bacterioplankton populations in the face of predicted climate-induced changes to the global ocean.