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BIOLOGICAL SCIENCES / ENVIRONMENTAL SCIENCES
Microbial community gene expression in ocean surface waters
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Departments of *Civil and Environmental Engineering and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139; Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA 16802
Edited by David M. Karl, University of Hawaii, Honolulu, HI, and approved January 22, 2008 (received for review September 19, 2007)
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
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.
To whom correspondence may be addressed. E-mail: delong{at}mit.edu or chisholm{at}mit.edu
© 2008 by The National Academy of Sciences of the USA
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