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Proc Natl Acad Sci U S A. 2014 Jul 29;111(30):11085-90. doi: 10.1073/pnas.1402782111. Epub 2014 Jul 14.

Microspatial gene expression patterns in the Amazon River Plume.

Author information

  • 1Departments of Microbiology and.
  • 2College of Earth, Ocean, and Atmospheric Science, Oregon State University, Corvallis, OR 97331;
  • 3Marine Sciences, University of Georgia, Athens, GA 30602;
  • 4College of Marine Science, University of South Florida, St. Petersburg, FL 33701;
  • 5Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD 21613; and.
  • 6Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA 92093.
  • 7Marine Sciences, University of Georgia, Athens, GA 30602; mmoran@uga.edu.

Abstract

We investigated expression of genes mediating elemental cycling at the microspatial scale in the ocean's largest river plume using, to our knowledge, the first fully quantitative inventory of genes and transcripts. The bacterial and archaeal communities associated with a phytoplankton bloom in Amazon River Plume waters at the outer continental shelf in June 2010 harbored ∼ 1.0 × 10(13) genes and 4.7 × 10(11) transcripts per liter that mapped to several thousand microbial genomes. Genomes from free-living cells were more abundant than those from particle-associated cells, and they generated more transcripts per liter for carbon fixation, heterotrophy, nitrogen and phosphorus uptake, and iron acquisition, although they had lower expression ratios (transcripts ⋅ gene(-1)) overall. Genomes from particle-associated cells contributed more transcripts for sulfur cycling, aromatic compound degradation, and the synthesis of biologically essential vitamins, with an overall twofold up-regulation of expression compared with free-living cells. Quantitatively, gene regulation differences were more important than genome abundance differences in explaining why microenvironment transcriptomes differed. Taxa contributing genomes to both free-living and particle-associated communities had up to 65% of their expressed genes regulated differently between the two, quantifying the extent of transcriptional plasticity in marine microbes in situ. In response to patchiness in carbon, nutrients, and light at the micrometer scale, Amazon Plume microbes regulated the expression of genes relevant to biogeochemical processes at the ecosystem scale.

KEYWORDS:

biogeochemistry; gene expression ratios; marine bacteria; metagenomics; metatranscriptomics

PMID:
25024226
[PubMed - in process]
PMCID:
PMC4121788
[Available on 2015/1/29]
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