title: Microspatial gene expression patterns in the Amazon River Plume.
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.
authors.affiliation: Departments of Microbiology and.
authors.forename: Brandon M
authors.initials: BM
authors.lastname: Satinsky
authors.affiliation: College of Earth, Ocean, and Atmospheric Science, Oregon State University, Corvallis, OR 97331;
authors.forename: Byron C
authors.initials: BC
authors.lastname: Crump
authors.affiliation: Marine Sciences, University of Georgia, Athens, GA 30602;
authors.forename: Christa B
authors.initials: CB
authors.lastname: Smith
authors.affiliation: Marine Sciences, University of Georgia, Athens, GA 30602;
authors.forename: Shalabh
authors.initials: S
authors.lastname: Sharma
authors.affiliation: College of Marine Science, University of South Florida, St. Petersburg, FL 33701;
authors.forename: Brian L
authors.initials: BL
authors.lastname: Zielinski
authors.affiliation: Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD 21613; and.
authors.forename: Mary
authors.initials: M
authors.lastname: Doherty
authors.affiliation: Marine Sciences, University of Georgia, Athens, GA 30602;
authors.forename: Jun
authors.initials: J
authors.lastname: Meng
authors.affiliation: Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA 92093.
authors.forename: Shulei
authors.initials: S
authors.lastname: Sun
authors.affiliation: Marine Sciences, University of Georgia, Athens, GA 30602;
authors.forename: Patricia M
authors.initials: PM
authors.lastname: Medeiros
authors.affiliation: College of Marine Science, University of South Florida, St. Petersburg, FL 33701;
authors.forename: John H
authors.initials: JH
authors.lastname: Paul
authors.affiliation: Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD 21613; and.
authors.forename: Victoria J
authors.initials: VJ
authors.lastname: Coles
authors.affiliation: Marine Sciences, University of Georgia, Athens, GA 30602;
authors.forename: Patricia L
authors.initials: PL
authors.lastname: Yager
authors.affiliation: Marine Sciences, University of Georgia, Athens, GA 30602; mmoran@uga.edu.
authors.forename: Mary Ann
authors.initials: MA
authors.lastname: Moran
mesh_terms: D001105:Archaea / Q000378:metabolism*; D001419:Bacteria / Q000378:metabolism*; D017753:Ecosystem; D019848:Gene Expression Regulation, Archaeal / Q000502:physiology*; D015964:Gene Expression Regulation, Bacterial / Q000502:physiology*; D045483:Rivers / Q000382:microbiology*; D014871:Water Microbiology
keywords: biogeochemistry; gene expression ratios; marine bacteria; metagenomics; metatranscriptomics