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Microbial community gene expression in ocean surface waters

Frias-Lopez, Jorge ; Shi, Yanmei ; Tyson, Gene W ; Coleman, Maureen L ; Schuster, Stephan C ; Chisholm, Sallie W ; DeLong, Edward F

Proceedings of the National Academy of Sciences - PNAS, 2008-03, Vol.105 (10), p.3805-3810 [Periódico revisado por pares]

United States: National Academy of Sciences

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Título:
Microbial community gene expression in ocean surface waters
Autor: Frias-Lopez, Jorge ; Shi, Yanmei ; Tyson, Gene W ; Coleman, Maureen L ; Schuster, Stephan C ; Chisholm, Sallie W ; DeLong, Edward F
Assuntos: Biological Sciences ; Complementary DNA ; DNA ; DNA, Bacterial - genetics ; DNA, Complementary - biosynthesis ; DNA, Complementary - genetics ; Gene expression ; Gene Expression Profiling ; Gene Expression Regulation, Bacterial ; Gene Library ; Genes ; Genes, Bacterial - genetics ; Genomes ; Genomics ; Marine ; Metabolic Networks and Pathways - genetics ; Metagenomics ; Microbiology ; Microorganisms ; Nucleic Acid Amplification Techniques ; Oceans ; Pacific Ocean ; Phylogeny ; Prochlorococcus ; Prochlorococcus - genetics ; Prochlorococcus - isolation & purification ; RNA ; RNA, Bacterial - genetics ; RNA, Messenger - genetics ; Seawater - microbiology ; Sequence Analysis, DNA ; Surface water
É parte de: Proceedings of the National Academy of Sciences - PNAS, 2008-03, Vol.105 (10), p.3805-3810
Notas: ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
USDOE
DoE/ER/64506-17
FG02-07ER64506
Edited by David M. Karl, University of Hawaii, Honolulu, HI, and approved January 22, 2008
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.
Descrição: 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 ([almost equal to]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.
Editor: United States: National Academy of Sciences
Idioma: Inglês

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Microbial community gene expression in ocean surface waters

Frias-Lopez, Jorge ; Shi, Yanmei ; Tyson, Gene W ; Coleman, Maureen L ; Schuster, Stephan C ; Chisholm, Sallie W ; DeLong, Edward F

United States: National Academy of Sciences

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