Skip to main content

Main menu

  • Home
  • Articles
    • Current
    • Special Feature Articles - Most Recent
    • Special Features
    • Colloquia
    • Collected Articles
    • PNAS Classics
    • List of Issues
  • Front Matter
    • Front Matter Portal
    • Journal Club
  • News
    • For the Press
    • This Week In PNAS
    • PNAS in the News
  • Podcasts
  • Authors
    • Information for Authors
    • Editorial and Journal Policies
    • Submission Procedures
    • Fees and Licenses
  • Submit
  • Submit
  • About
    • Editorial Board
    • PNAS Staff
    • FAQ
    • Accessibility Statement
    • Rights and Permissions
    • Site Map
  • Contact
  • Journal Club
  • Subscribe
    • Subscription Rates
    • Subscriptions FAQ
    • Open Access
    • Recommend PNAS to Your Librarian

User menu

  • Log in
  • My Cart

Search

  • Advanced search
Home
Home
  • Log in
  • My Cart

Advanced Search

  • Home
  • Articles
    • Current
    • Special Feature Articles - Most Recent
    • Special Features
    • Colloquia
    • Collected Articles
    • PNAS Classics
    • List of Issues
  • Front Matter
    • Front Matter Portal
    • Journal Club
  • News
    • For the Press
    • This Week In PNAS
    • PNAS in the News
  • Podcasts
  • Authors
    • Information for Authors
    • Editorial and Journal Policies
    • Submission Procedures
    • Fees and Licenses
  • Submit
Research Article

Microbial community gene expression in ocean surface waters

Jorge Frias-Lopez, Yanmei Shi, Gene W. Tyson, Maureen L. Coleman, Stephan C. Schuster, Sallie W. Chisholm, and Edward F. DeLong
  1. Departments of *Civil and Environmental Engineering and
  2. §Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139;
  3. †Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA 16802

See allHide authors and affiliations

PNAS March 11, 2008 105 (10) 3805-3810; first published March 3, 2008; https://doi.org/10.1073/pnas.0708897105
Jorge Frias-Lopez
Departments of *Civil and Environmental Engineering and
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Yanmei Shi
Departments of *Civil and Environmental Engineering and
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Gene W. Tyson
Departments of *Civil and Environmental Engineering and
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Maureen L. Coleman
Departments of *Civil and Environmental Engineering and
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Stephan C. Schuster
†Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA 16802
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Sallie W. Chisholm
Departments of *Civil and Environmental Engineering and
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: delong@mit.edu chisholm@mit.edu
Edward F. DeLong
Departments of *Civil and Environmental Engineering and
§Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: delong@mit.edu chisholm@mit.edu
  1. Edited by David M. Karl, University of Hawaii, Honolulu, HI, and approved January 22, 2008 (received for review September 19, 2007)

  • Article
  • Figures & SI
  • Info & Metrics
  • PDF
Loading

Abstract

Metagenomics is expanding our knowledge of the gene content, functional significance, and genetic variability in natural microbial communities. Still, there exists limited information concerning the regulation and dynamics of genes in the environment. We report here global analysis of expressed genes in a naturally occurring microbial community. We first adapted RNA amplification technologies to produce large amounts of cDNA from small quantities of total microbial community RNA. The fidelity of the RNA amplification procedure was validated with Prochlorococcus cultures and then applied to a microbial assemblage collected in the oligotrophic Pacific Ocean. Microbial community cDNAs were analyzed by pyrosequencing and compared with microbial community genomic DNA sequences determined from the same sample. Pyrosequencing-based estimates of microbial community gene expression compared favorably to independent assessments of individual gene expression using quantitative PCR. Genes associated with key metabolic pathways in open ocean microbial species—including genes involved in photosynthesis, carbon fixation, and nitrogen acquisition—and a number of genes encoding hypothetical proteins were highly represented in the cDNA pool. Genes present in the variable regions of Prochlorococcus genomes were among the most highly expressed, suggesting these encode proteins central to cellular processes in specific genotypes. Although many transcripts detected were highly similar to genes previously detected in ocean metagenomic surveys, a significant fraction (≈50%) were unique. Thus, microbial community transcriptomic analyses revealed not only indigenous gene- and taxon-specific expression patterns but also gene categories undetected in previous DNA-based metagenomic surveys.

  • bacterial communities
  • metagenomics
  • metatranscriptomics
  • marine
  • cDNA

Footnotes

  • ↵‡To whom correspondence may be addressed. E-mail: delong{at}mit.edu or chisholm{at}mit.edu
  • Author contributions: J.F.-L. and Y.S. contributed equally to this work. J.F.-L., Y.S., G.W.T., S.W.C., and E.F.D. designed research; Y.S. performed research; S.C.S. contributed new reagents/analytic tools; J.F.-L., Y.S., G.W.T., M.L.C., S.W.C., and E.F.D. analyzed data; and J.F.-L., Y.S., G.W.T., M.L.C., S.W.C., and E.F.D. wrote the paper.

  • The authors declare no conflict of interest.

  • This article is a PNAS Direct Submission.

  • Data deposition: DNA and cDNA sequences reported in this paper have been deposited in the GenBank database (accession nos. SRA000262 and SRA000263).

  • This article contains supporting information online at www.pnas.org/cgi/content/full/0708897105/DC1.

  • Received September 19, 2007.
  • © 2008 by The National Academy of Sciences of the USA

Freely available online through the PNAS open access option.

View Full Text
PreviousNext
Back to top
Article Alerts
Email Article

Thank you for your interest in spreading the word on PNAS.

NOTE: We only request your email address so that the person you are recommending the page to knows that you wanted them to see it, and that it is not junk mail. We do not capture any email address.

Enter multiple addresses on separate lines or separate them with commas.
Microbial community gene expression in ocean surface waters
(Your Name) has sent you a message from PNAS
(Your Name) thought you would like to see the PNAS web site.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Citation Tools
Microbial community gene expression in ocean surface waters
Jorge Frias-Lopez, Yanmei Shi, Gene W. Tyson, Maureen L. Coleman, Stephan C. Schuster, Sallie W. Chisholm, Edward F. DeLong
Proceedings of the National Academy of Sciences Mar 2008, 105 (10) 3805-3810; DOI: 10.1073/pnas.0708897105

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
Request Permissions
Share
Microbial community gene expression in ocean surface waters
Jorge Frias-Lopez, Yanmei Shi, Gene W. Tyson, Maureen L. Coleman, Stephan C. Schuster, Sallie W. Chisholm, Edward F. DeLong
Proceedings of the National Academy of Sciences Mar 2008, 105 (10) 3805-3810; DOI: 10.1073/pnas.0708897105
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
  • Tweet Widget
  • Facebook Like
  • Mendeley logo Mendeley

Related Article

  • In This Issue
    - Mar 11, 2008
Proceedings of the National Academy of Sciences: 105 (10)
Table of Contents

Submit

Sign up for Article Alerts

Jump to section

  • Article
    • Abstract
    • Results and Discussion
    • Materials and Methods
    • Acknowledgments
    • Footnotes
    • References
  • Figures & SI
  • Info & Metrics
  • PDF

You May Also be Interested in

Surgeons hands during surgery
Inner Workings: Advances in infectious disease treatment promise to expand the pool of donor organs
Despite myriad challenges, clinicians see room for progress.
Image credit: Shutterstock/David Tadevosian.
Setting sun over a sun-baked dirt landscape
Core Concept: Popular integrated assessment climate policy models have key caveats
Better explicating the strengths and shortcomings of these models will help refine projections and improve transparency in the years ahead.
Image credit: Witsawat.S.
Double helix
Journal Club: Noncoding DNA shown to underlie function, cause limb malformations
Using CRISPR, researchers showed that a region some used to label “junk DNA” has a major role in a rare genetic disorder.
Image credit: Nathan Devery.
Steamboat Geyser eruption.
Eruption of Steamboat Geyser
Mara Reed and Michael Manga explore why Yellowstone's Steamboat Geyser resumed erupting in 2018.
Listen
Past PodcastsSubscribe
Birds nestling on tree branches
Parent–offspring conflict in songbird fledging
Some songbird parents might improve their own fitness by manipulating their offspring into leaving the nest early, at the cost of fledgling survival, a study finds.
Image credit: Gil Eckrich (photographer).

Similar Articles

Site Logo
Powered by HighWire
  • Submit Manuscript
  • Twitter
  • Facebook
  • RSS Feeds
  • Email Alerts

Articles

  • Current Issue
  • Special Feature Articles – Most Recent
  • List of Issues

PNAS Portals

  • Anthropology
  • Chemistry
  • Classics
  • Front Matter
  • Physics
  • Sustainability Science
  • Teaching Resources

Information

  • Authors
  • Editorial Board
  • Reviewers
  • Subscribers
  • Librarians
  • Press
  • Site Map
  • PNAS Updates
  • FAQs
  • Accessibility Statement
  • Rights & Permissions
  • About
  • Contact

Feedback    Privacy/Legal

Copyright © 2021 National Academy of Sciences. Online ISSN 1091-6490