jdmagasin/ucyn-a-metatranscriptomes

UCYN-A Metatranscriptomes at Stn. ALOHA and Scripps Pier

Key scripts and data files for Open ocean and coastal strains of the N₂-fixing cyanobacterium UCYN-A have distinct transcriptomes by María del Carmen Muñoz-Marín, Jonathan D. Magasin, and Jonathan P. Zehr. This paper was published in PLOS ONE on May 2, 2023.

Biologically usable forms of nitrogen are scarce over much of the world ocean. Thus, marine microbes that can fix atmospheric N₂ gas into usable ammonia (NH₃) are critical to marine food webs. One such microbe, the N₂-fixing, the endosymbiotic cyanobacterium Candidatus Atelocyanobacterium thalassa ("UCYN-A"), can contribute substantial amounts of fixed nitrogen to marine microbial communities. UCYN-A genomes are highly streamlined and lack the full complement of genes required for obtaining carbon through photosynthesis. Instead UCYN-A obtains carbon from its haptophyte (photosynthetic) host in exchange for fixed nitrogen.

Our study compared metatranscriptomes from natural populations of UCYN-A that were collected from two very different habitats, the nutrient-poor North Pacific Subtropical Gyre (at Stn. ALOHA) and the nutrient-rich waters off the California coast (at Scripps Pier). For our study, metatranscritomes were obtained for samples collected over ~2-days with 3 to 6 hours between samples in order to study day-night gene expression patterns. Differences in expression patterns across habitats can improve our understanding of UCYN-A ecotypes and their hosts, which differ among sublineages.

The Scripps Pier metatranscriptomes were previously reported by Muñoz-Marín et al. (2019). The Stn. ALOHA data are new. Both studies used custom UCYN-A microarrays that targeted major UCYN-A ecotypes UCYN-A1 (open ocean) and UCYN-A2 (coastal). The Stn. ALOHA data used an updated microarray design that included known genes for UCYN-A3 (open ocean).

Repository contents:

• scripts/

  • runMicroTOOLsPipeine.R: Runs the MicroTOOLs microarray pipeline on the Stn. ALOHA arrays. This is provided to illustrate the major steps for processing the arrays from quality control through robust multi-array averaging and the identification of genes with significant 24 h periodic expression. Main outputs from running the pipeline are provided in Data/workspace.Rdata.
  • findCyclicGenes.R: This is run by the previous script to identify genes with significant 24 h periodic expression ("diel genes").
  • statistical_tests.R: Interactive script that does statistical tests that appear in our publication. Relies on Data/workspace.Rdata.

• Metadata/: Includes the main configuration file that was used to run runMicroTOOLsPipeline.R and two other files that describe the Stn. ALOHA data. Note that the Stn. ALOHA data reside at the NCBI Gene Expression Omnibus under accession GSE206403.

• Data/workspace.Rdata: R image that has the Stn. ALOHA and Scripps Pier ExpressionSets and other key objects used during the analysis.

• Logs/: Includes the log files from runMicroTOOLsPipeline.R and findCyclicGenes.R that are associated with the final data analyzed for the publication.