Molecular Environmental Science

Molecule Hunters

Metabolites from cultured microorganisms

We are applying cutting-edge mass spectrometry to better understand metabolic dynamics of individual marine microorganisms. Our goal is to connect cellular metabolism to biogeochemical cycles by analyzing intracellular and extracellular metabolic profiles from organisms in culture. We have several ecologically important marine microbes in culture including, Thalassiosira pseudonana (centric diatom), Ruegeria pomeroyi (heterotrophic alpha-proteobacteria), Synechococcus elongatus (cyanobacteria), and Micromonas pusilla (picoeukaryote). We can then ask specific questions that probe the metabolic response of organisms to different growth conditions (e.g., nutrient availability and organic substrates). Data generated in these experiments help us understand the factors that influence chemically-mediated microbial interactions and the production and transformation of dissolved organic matter. In addition, results from our culture experiments complement field studies by identifying potential target metabolites and guiding interpretation of environmental metabolite distributions.

Some compounds that we found to be biochemically and ecologically relevant but have not been previously quantified in the ocean:

  • Kynurenine: amino acid and oxidation product of tryptophan
  • Thymidine: nucleoside, many heterotrophic organisms incorporate this into DNA
  • Indole 3-acetic acid: tryptophan degradation product and plant growth hormone
  • N-Acetylchitotriose: polysaccharide, precursor to chitin which is an abundant biopolymer found in cell walls of fungi and exoskeletons of crustaceans
  • 5’-Deoxy-5’-(methylthio)adenosine: intermediate in the methionine salvage pathway, by-product of acyl homoserine lactone and spermidine synthesis
  • Alpha ribazole: a component of the nucleotide loop of Vitamin B12

This work is funded by NSF and The Gordon and Betty Moore Foundation.

Recent publications:

Kujawinski, E.B., K. Longnecker, H. Alexander, S.T. Dyhrman, C.L. Fiore, S.T. Haley, and W.M. Johnson (2017). Phosphorus availability regulates intracellular nucleotides in marine eukaryotic phytoplankton. Limnology and Oceanography Letters. (

Johnson, W.M., M.C. Kido Soule and E.B. Kujawinski (2016). Evidence for quorum sensing and differential metabolite production by a marine bacterium in response to DMSP.ISME Journal

Fiore, C. L., K. Longnecker, M. C. Kido Soule and E. B. Kujawinski (2015). Release of ecologically relevant metabolites by the cyanobacterium, Synechococcus elongatus CCMP 1631. Environmental Microbiology 17:3949-3963.

Longnecker, K., M. C. Kido Soule and E. B. Kujawinski (2015). Dissolved organic matter produced by Thalassiosira pseudonana. Marine Chemistry 168: 114-123.

Last updated: June 12, 2017