Ecology of uncultured Prochlorococcus clades revealed through single-cell genomics and biogeographic analysis

Rex R. Malmstrom, Sébastien Rodrigue, Katherine H. Huang, Libusha Kelly, Suzanne E. Kern, Anne Thompson, Sara Roggensack, Paul M. Berube, Matthew R. Henn, Sallie W. Chisholm

Research output: Contribution to journalArticle

48 Citations (Scopus)

Abstract

Prochlorococcus is the numerically dominant photosynthetic organism throughout much of the worlds oceans, yet little is known about the ecology and genetic diversity of populations inhabiting tropical waters. To help close this gap, we examined natural Prochlorococcus communities in the tropical Pacific Ocean using a single-cell whole-genome amplification and sequencing. Analysis of the gene content of just 10 single cells from these waters added 394 new genes to the Prochlorococcus pan-genome - that is, genes never before seen in a Prochlorococcus cell. Analysis of marker genes, including the ribosomal internal transcribed sequence, from dozens of individual cells revealed several representatives from two uncultivated clades of Prochlorococcus previously identified as HNLC1 and HNLC2. While the HNLC clades can dominate Prochlorococcus communities under certain conditions, their overall geographic distribution was highly restricted compared with other clades of Prochlorococcus. In the Atlantic and Pacific oceans, these clades were only found in warm waters with low Fe and high inorganic P levels. Genomic analysis suggests that at least one of these clades thrives in low Fe environments by scavenging organic-bound Fe, a process previously unknown in Prochlorococcus. Furthermore, the capacity to utilize organic-bound Fe appears to have been acquired horizontally and may be exchanged among other clades of Prochlorococcus. Finally, one of the single Prochlorococcus cells sequenced contained a partial genome of what appears to be a prophage integrated into the genome.

Original languageEnglish (US)
Pages (from-to)184-198
Number of pages15
JournalISME Journal
Volume7
Issue number1
DOIs
StatePublished - Jan 2013
Externally publishedYes

Fingerprint

Prochlorococcus
Genomics
Ecology
genomics
genome
ecology
gene
ocean
cells
Genome
Pacific Ocean
warm water
amplification
Genes
Water
water
analysis
Atlantic Ocean
Prophages
genes

Keywords

  • HNLC
  • Prochlorococcus
  • siderophore

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Microbiology

Cite this

Malmstrom, R. R., Rodrigue, S., Huang, K. H., Kelly, L., Kern, S. E., Thompson, A., ... Chisholm, S. W. (2013). Ecology of uncultured Prochlorococcus clades revealed through single-cell genomics and biogeographic analysis. ISME Journal, 7(1), 184-198. https://doi.org/10.1038/ismej.2012.89

Ecology of uncultured Prochlorococcus clades revealed through single-cell genomics and biogeographic analysis. / Malmstrom, Rex R.; Rodrigue, Sébastien; Huang, Katherine H.; Kelly, Libusha; Kern, Suzanne E.; Thompson, Anne; Roggensack, Sara; Berube, Paul M.; Henn, Matthew R.; Chisholm, Sallie W.

In: ISME Journal, Vol. 7, No. 1, 01.2013, p. 184-198.

Research output: Contribution to journalArticle

Malmstrom, RR, Rodrigue, S, Huang, KH, Kelly, L, Kern, SE, Thompson, A, Roggensack, S, Berube, PM, Henn, MR & Chisholm, SW 2013, 'Ecology of uncultured Prochlorococcus clades revealed through single-cell genomics and biogeographic analysis', ISME Journal, vol. 7, no. 1, pp. 184-198. https://doi.org/10.1038/ismej.2012.89
Malmstrom, Rex R. ; Rodrigue, Sébastien ; Huang, Katherine H. ; Kelly, Libusha ; Kern, Suzanne E. ; Thompson, Anne ; Roggensack, Sara ; Berube, Paul M. ; Henn, Matthew R. ; Chisholm, Sallie W. / Ecology of uncultured Prochlorococcus clades revealed through single-cell genomics and biogeographic analysis. In: ISME Journal. 2013 ; Vol. 7, No. 1. pp. 184-198.
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