Original Article

Subject Category: Microbial ecology and functional diversity of natural habitats

The ISME Journal (2009) 3, 618–631; doi:10.1038/ismej.2009.8; published online 19 February 2009

In situ transcriptomic analysis of the globally important keystone N2-fixing taxon Crocosphaera watsonii

Ian Hewson1, Rachel S Poretsky2, Roxanne A Beinart1,5, Angelicque E White3, Tuo Shi1,6, Shellie R Bench1, Pia H Moisander1, Ryan W Paerl1, H James Tripp1, Joseph P Montoya4, Mary Ann Moran2 and Jonathan P Zehr1

  1. 1Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, USA
  2. 2Department of Marine Science, University of Georgia, Athens, GA, USA
  3. 3College of Oceanic and Atmospheric Sciences, Oregon State University, Corvallis, OR, USA
  4. 4Georgia Institute of Technology, School of Biology, Atlanta, GA, USA

Correspondence: I Hewson, Department of Microbiology, Cornell University, Wing Hall 403, Ithaca, NY 14853, USA. E-mail: hewson@cornell.edu

5Current address: Department of Organismal and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.

6Current address: Algenol Biofuels, 1700 Union Ave, Baltimore, MD 21211, USA.

Received 27 October 2008; Revised 12 January 2009; Accepted 12 January 2009; Published online 19 February 2009.



The diazotrophic cyanobacterium Crocosphaera watsonii supplies fixed nitrogen (N) to N-depleted surface waters of the tropical oceans, but the factors that determine its distribution and contribution to global N2 fixation are not well constrained for natural populations. Despite the heterogeneity of the marine environment, the genome of C. watsonii is highly conserved in nucleotide sequence in contrast to sympatric planktonic cyanobacteria. We applied a whole assemblage shotgun transcript sequencing approach to samples collected from a bloom of C. watsonii observed in the South Pacific to understand the genomic mechanisms that may lead to high population densities. We obtained 999 C. watsonii transcript reads from two metatranscriptomes prepared from mixed assemblage RNA collected in the day and at night. The C. watsonii population had unexpectedly high transcription of hypothetical protein genes (31% of protein-encoding genes) and transposases (12%). Furthermore, genes were expressed that are necessary for living in the oligotrophic ocean, including the nitrogenase cluster and the iron-stress-induced protein A (isiA) that functions to protect photosystem I from high-light-induced damage. C. watsonii transcripts retrieved from metatranscriptomes at other locations in the southwest Pacific Ocean, station ALOHA and the equatorial Atlantic Ocean were similar in composition to those recovered in the enriched population. Quantitative PCR and quantitative reverse transcriptase PCR were used to confirm the high expression of these genes within the bloom, but transcription patterns varied at shallower and deeper horizons. These data represent the first transcript study of a rare individual microorganism in situ and provide insight into the mechanisms of genome diversification and the ecophysiology of natural populations of keystone organisms that are important in global nitrogen cycling.


metatranscriptome, Crocosphaera, gene expression, transposase, diazotroph, oligotrophic