Microbial community gene expression in ocean surface waters

Frias-Lopez, Jorge, Shi,Yanmei, Tyson, Gene, Coleman, Maureen, Schuster, Stephan, Chisholm, Sallie and DeLong, Edward (2008) Microbial community gene expression in ocean surface waters. Proceedings of the National Academy of Sciences of the United States of America, 105 10: 3805-3810. doi:10.1073/pnas.0708897105


Author Frias-Lopez, Jorge
Shi,Yanmei
Tyson, Gene
Coleman, Maureen
Schuster, Stephan
Chisholm, Sallie
DeLong, Edward
Title Microbial community gene expression in ocean surface waters
Journal name Proceedings of the National Academy of Sciences of the United States of America   Check publisher's open access policy
ISSN 0027-8424
1091-6490
Publication date 2008-03-11
Sub-type Article (original research)
DOI 10.1073/pnas.0708897105
Open Access Status Not Open Access
Volume 105
Issue 10
Start page 3805
End page 3810
Total pages 6
Place of publication Washington, USA
Publisher National Academy of Sciences of the U.S.A
Language eng
Subject 0605 Microbiology
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.
Keyword Bacterial communities
Metatranscriptomics
Metagenomics
cDNA
Q-Index Code C1
Q-Index Status Provisional Code

Document type: Journal Article
Sub-type: Article (original research)
Collections: Excellence in Research Australia (ERA) - Collection
School of Chemistry and Molecular Biosciences
 
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