Table of Contents

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

The CSV file available here describes the samples, methods, and fastq files for raw data available from the Joint Genome Institute (JGI) at https://data.jgi.doe.gov. The data in JGI can be found under the following project ID numbers: 1290093, 1290172, 1290174, 1317772, 1317774, 1317776, 1317778, and 1334780.

Laboratory studies were carried out at the University of Georgia, Athens, GA, USA. The studies took place over the following dates:
Thalassiosira: 1-7th July 2020
Synechococcus: 16-23rd Feb 2021
Emiliania: 18-28th May 2021

Emiliania huxleyi CCMP151
A laboratory study was conducted using cultures of a marine coccolithophore (Emiliania huxleyi CCMP151) and heterotrophic bacterium, Ruegeria pomeroyi. Coccolithophore cultures were pre-acclimated to three temperature treatments (15°, 20°, and 28° Celsius) and grown co-cultures. The transcriptome treatments consisted of axenic coccolithophore, the coccolithophore with the bacterium, and the bacterium with the coccolithophore, and three replicates were analyzed at each sample point. Stranded RNA-Seq libraries were sequenced using an Illumina NovaSeq instrument. For co-cultures, E. huxleyi and bacterial cells were separated by filtration prior to RNA extraction.

Thalassiosira pseudonana CCMP1335
A laboratory study was conducted using cultures of a marine diatom (Thalassiosira pseudonana CCMP1335) and heterotrophic bacterium, Ruegeria pomeroyi. Diatom cultures were pre-acclimated to three temperature treatments (14°, 20°, and 28° Celsius) and grown as co-cultures. The transcriptome treatments consisted of axenic diatom, the diatom with the bacterium, and the bacterium with the diatom, and three replicates were analyzed at each sample point. Stranded RNA-Seq libraries were sequenced using an Illumina NovaSeq instrument. For co-cultures, diatom and bacterial cells were separated by filtration prior to RNA extraction.

Synechococcus sp. WH8102
A laboratory study was conducted using cultures of a marine cyanobacterium (Synechococcus sp. WH8102 and heterotrophic bacterium, Ruegeria pomeroyi. Synechococcus cultures were pre-acclimated to three temperature treatments (20°, 24°, and 28° Celsius) and grown as co-cultures. The transcriptome treatments consisted of axenic Synechococcus, Synechococcus with the heterotrophic bacterium, and the bacterium with the Synechococcus, and three replicates were analyzed at each sample point. Stranded RNA-Seq libraries were sequenced using an Illumina NovaSeq instrument. RNA extraction of co-cultures was carried out without prefiltration, and transcripts were separated at mapping.

Raw reads, mapped read counts, and quality control checks were performed at JGI and are available on the JGI Data portal.

- imported three original data files into the BCO-DMO system: Ehux.txt, Tpseudo.txt, Syn.txt.
- concatenated the three files into one data file.
- renamed fields to comply with BCO-DMO naming conventions.
- named the final data file "905306_v1_transcriptomes.csv".

NSF Award Abstract:
Phytoplankton in the surface ocean are responsible for roughly half of all photosynthesis on the planet. Much of the organic material created by these photosynthetic organisms is ultimately consumed by diverse marine bacteria with differing preferences for specific types of chemical compounds. This project investigates how climate change (temperature and CO2) might alter the types and amounts of organic compounds produced by different species of marine phytoplankton and the types and amounts of compounds transferred from phytoplankton to marine bacteria. Shifts in organic compounds transferred to bacteria could alter the distribution of bacterial species in the ocean, their growth rates and efficiencies, and flows of energy through the global ocean. This project helps scientists better understand the effects of climate change on marine ecosystems. Two graduate students and a postdoctoral researcher are supported by the project, receiving interdisciplinary training in biology, chemistry, and ocean sciences. Summer research internships in the PIs' laboratories are offered to AP Biology students enrolled at Cedar Shoals High School in Athens, GA, a school that serves a diverse social and economic community.

Much of the bacterial secondary production in the surface ocean is supported by rapid uptake of labile metabolites released from phytoplankton, either directly through excretion and diffusion or indirectly through lysis and predation. This project investigates the effects of two climate change variables (temperature and CO2) on the metabolite pools produced and released by three model phytoplankton species (a diatom, a coccolithophore, and a cyanobacterium) and assesses changes in the composition and fate of metabolites transferred to bacteria. Phytoplankton species are being grown axenically at two different temperatures and CO2 concentrations in a factorial design and endo- and exometabolite composition is determined using NMR. A suite of phytoplankton physiological characteristics is measured and evaluated in the context of metabolite composition. Experiments with heterotrophic bacteria (either model bacteria or natural bacterial communities) are being conducted to assess the effects of climate change variables on metabolite transfer from phytoplankton to marine bacteria. In the first experiment type, bacteria are co-cultured with the phytoplankton at different temperatures and CO2 concentrations, and changes in bacterial gene expression and metabolite concentrations are used to assess shifts in the composition of metabolites transferred. In the second type, bacteria are grown on phytoplankton metabolite pools produced at different temperatures and CO2 concentrations in high-throughput bioassays, and changes in bacterial traits (growth rate, carrying capacity, growth efficiency) resulting from the different climate scenarios are used to indicate changes in metabolite quality. Knowledge of how the heterotrophic processing of phytoplankton metabolites might shift in response to climate change allows better prediction of Earth's future carbon cycle.

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.