Coordinated gene expression between Trichodesmium and its microbiome over day–night cycles in the North Pacific Subtropical Gyre

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Trichodesmium is a widespread, N2 fixing marine cyanobacterium that drives inputs of newly fixed nitrogen and carbon into the oligotrophic ecosystems where it occurs. Colonies of Trichodesmium ubiquitously occur with heterotrophic bacteria that make up a diverse microbiome, and interactions within this Trichodesmium holobiont could influence the fate of fixed carbon and nitrogen. Metatranscriptome sequencing was performed on Trichodesmium colonies collected during high-frequency Lagrangian sampling in the North Pacific Subtropical Gyre (NPSG) to identify possible interactions between the Trichodesmium host and microbiome over day–night cycles. Here we show significantly coordinated patterns of gene expression between host and microbiome, many of which had significant day–night periodicity. The functions of the co-expressed genes suggested a suite of interactions within the holobiont linked to key resources including nitrogen, carbon, and iron. Evidence of microbiome reliance on Trichodesmium-derived vitamin B12 was also detected in co-expression patterns, highlighting a dependency that could shape holobiont community structure. Collectively, these patterns of expression suggest that biotic interactions could influence colony cycling of resources like nitrogen and vitamin B12, and decouple activities, like N2 fixation, from typical abiotic drivers of Trichodesmium physiological ecology.

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We thank the scientists who worked collaboratively on the 2015 research expedition as part of the Simons Collaboration on Ocean Processes and Ecology (SCOPE). For assistance at sea, we thank the captain and crew of the R/V Kilo Moana, and Samuel Wilson for serving as chief scientist. We also thank Frank Aylward for assistance with statistical analyses and Matthew Harke, Mónica Rouco, Katherine Heal, and Harriet Alexander for helpful discussions of the data. Finally, we thank the three anonymous reviewers whose comments and suggestions strengthened the manuscript. This research was funded by the Simons Foundation (SCOPE award ID 329108 to STD), and is a contribution of SCOPE. KRF was partially supported by a National Science Foundation Graduate Research Fellowship (DGE-16-44869).

Author contributions

KRF and STD designed the study. All authors carried out sampling. KRF performed lab work and analyzed the data. KRF and STD wrote the manuscript with input from STH.

Author information


  1. Department of Earth and Environmental Sciences, Columbia University, New York, NY, 10025, USA

    • Kyle R Frischkorn
    •  & Sonya T Dyhrman
  2. Lamont-Doherty Earth Observatory, Palisades, NY, 10964, USA

    • Kyle R Frischkorn
    • , Sheean T Haley
    •  & Sonya T Dyhrman


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Conflict of interest

The authors declare that they have no conflict of interest.

Corresponding author

Correspondence to Sonya T Dyhrman.

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