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


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2012-08-16

AUTHORS

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

ABSTRACT

Prochlorococcus is the numerically dominant photosynthetic organism throughout much of the world’s 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. More... »

PAGES

184-198

References to SciGraph publications

  • 2010-12-02. A novel clade of Prochlorococcus found in high nutrient low chlorophyll waters in the South and Equatorial Pacific Ocean in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2010-05-13. Temporal dynamics of Prochlorococcus ecotypes in the Atlantic and Pacific oceans in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2003-08. Cyanophages infecting the oceanic cyanobacterium Prochlorococcus in NATURE
  • 1994-09. Testing the iron hypothesis in ecosystems of the equatorial Pacific Ocean in NATURE
  • 2009-11-01. Large-scale distribution of Atlantic nitrogen fixation controlled by iron availability in NATURE GEOSCIENCE
  • 2011-05-12. Transcriptome response of high- and low-light-adapted Prochlorococcus strains to changing iron availability in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2011-09-29. Novel lineages of Prochlorococcus and Synechococcus in the global oceans in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2005-07-31. Genome sequencing in microfabricated high-density picolitre reactors in NATURE
  • 2007-09. Genome-wide expression dynamics of a marine virus and host reveal features of co-evolution in NATURE
  • 2003-08-13. Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation in NATURE
  • 1999-05. The role of trace metals in photosynthetic electron transport in O2-evolving organisms in PHOTOSYNTHESIS RESEARCH
  • 2001-06. Three-dimensional structure of cyanobacterial photosystem I at 2.5 Å resolution in NATURE
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/ismej.2012.89

    DOI

    http://dx.doi.org/10.1038/ismej.2012.89

    DIMENSIONS

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    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/22895163


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