Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities.

PloS One
Jack A GilbertIan Joint

Abstract

Sequencing the expressed genetic information of an ecosystem (metatranscriptome) can provide information about the response of organisms to varying environmental conditions. Until recently, metatranscriptomics has been limited to microarray technology and random cloning methodologies. The application of high-throughput sequencing technology is now enabling access to both known and previously unknown transcripts in natural communities. We present a study of a complex marine metatranscriptome obtained from random whole-community mRNA using the GS-FLX Pyrosequencing technology. Eight samples, four DNA and four mRNA, were processed from two time points in a controlled coastal ocean mesocosm study (Bergen, Norway) involving an induced phytoplankton bloom producing a total of 323,161,989 base pairs. Our study confirms the finding of the first published metatranscriptomic studies of marine and soil environments that metatranscriptomics targets highly expressed sequences which are frequently novel. Our alternative methodology increases the range of experimental options available for conducting such studies and is characterized by an exceptional enrichment of mRNA (99.92%) versus ribosomal RNA. Analysis of corresponding metagenomes conf...Continue Reading

References

Nov 2, 2002·BMC Evolutionary Biology·David J LipmanTatiana A Tatusova
Jul 8, 2005·Applied and Environmental Microbiology·Rachel S PoretskyJames T Hollibaugh
Oct 11, 2005·Nucleic Acids Research·Ross OverbeekVeronika Vonstein
May 30, 2006·Nature Biotechnology·Kun ZhangGeorge M Church
Aug 18, 2006·Nature·S LeiningerC Schleper
Nov 23, 2006·Journal of Microbiological Methods·Patrice FrancoisJacques Schrenzel
Jan 16, 2007·Environmental Microbiology·Víctor ParroElena González-Toril
Mar 16, 2007·PLoS Biology·Rekha SeshadriMarvin Frazier
Dec 7, 2007·The Journal of Clinical Endocrinology and Metabolism·David J Handelsman
Feb 12, 2008·BMC Genomics·Ramy K AzizOlga Zagnitko
Mar 5, 2008·Proceedings of the National Academy of Sciences of the United States of America·Jorge Frias-LopezEdward F Delong
May 2, 2008·Omics : a Journal of Integrative Biology·Susanna-Assunta SansoneUNKNOWN Members of the RSBI Working Group
May 10, 2008·Nature Biotechnology·Dawn FieldAnil Wipat
Sep 12, 2008·Environmental Microbiology·Jack A GilbertIan Joint
Feb 7, 2009·Environmental Microbiology·Kristina SchaussChrista Schleper

❮ Previous
Next ❯

Citations

Jan 25, 2013·Proceedings of the National Academy of Sciences of the United States of America·Elizabeth A OttesenEdward F DeLong
Feb 19, 2011·Annual Review of Marine Science·Jack A Gilbert, Christopher L Dupont
Feb 26, 2011·Archaea : an International Microbiological Journal·Jasper WaltherJohn van der Oost
Sep 18, 2009·Applied Microbiology and Biotechnology·Carola Simon, Rolf Daniel
Oct 28, 2009·Cellular and Molecular Life Sciences : CMLS·Samuel Marguerat, Jürg Bähler
Nov 17, 2009·BMC Genomics·Katharina J Hoff
Apr 15, 2010·BMC Bioinformatics·Beifang NiuWeizhong Li
May 21, 2010·Genome Biology·Claudia SteglichSallie W Chisholm
Jul 14, 2010·Applied and Environmental Microbiology·Carsten MettelWerner Liesack
Sep 2, 2010·PloS One·Valeriy PoroykoMichael J Morowitz
Sep 3, 2010·Proceedings of the National Academy of Sciences of the United States of America·Jay McCarrenEdward F DeLong
Sep 17, 2010·The ISME Journal·Scott M GiffordMary Ann Moran
Sep 21, 2010·Applied and Environmental Microbiology·Ken C McGrathPeer M Schenk
Nov 26, 2010·The ISME Journal·Jack A GilbertMark J Bailey
Dec 21, 2010·Applied and Environmental Microbiology·Carola Simon, Rolf Daniel
Mar 5, 2011·BMC Bioinformatics·Suparna MitraDaniel H Huson
Mar 17, 2011·PloS One·María José GosalbesAndrés Moya
Apr 7, 2011·MBio·Lindsey BomarJoerg Graf
Sep 2, 2011·Nucleic Acids Research·Hana YiJongsik Chun
Oct 4, 2011·PloS One·Thomas C JeffriesJames G Mitchell
Mar 6, 2012·BMC Genomics·Atsushi OguraSatoshi Nagai
Oct 12, 2012·The ISME Journal·Omri M FinkelShimshon Belkin
Jan 10, 2013·PLoS Computational Biology·Xochitl C Morgan, Curtis Huttenhower
Feb 9, 2013·BMC Evolutionary Biology·Bhakti DwivediMya Breitbart
Apr 23, 2013·Microbial Ecology·Karen E Nelson
Oct 30, 2009·Briefings in Bioinformatics·David Stephen HornerGraziano Pesole
Jul 10, 2012·Briefings in Bioinformatics·Weizhong LiJohn Wooley
Apr 26, 2012·Nucleic Acids Research·Norman J MacDonaldRobert G Beiko
Jan 1, 2009·Journal of Computer Science and Technology·John C Wooley, Yuzhen Ye
Apr 7, 2010·Analytical and Bioanalytical Chemistry·Kristin SchirmerSmitha Pillai

❮ Previous
Next ❯

Datasets Mentioned

BETA
GSE10119
SRA000266

Methods Mentioned

BETA
nucleic acid extraction
chip
PCR
electrophoresis

Software Mentioned

EST
CAMERA
SEED
BLASTN
RAST
BLAST
CD
GenomiPHI
MG
HIT

Related Concepts

Related Feeds

ATP Synthases

ATP synthases are enzymes located in the inner mitochondrial membrane that catalyze the synthesis of ATP during cellular respiration. Discover the latest research on ATP synthases here.

Birth Defects

Birth defects encompass structural and functional alterations that occur during embryonic or fetal development and are present since birth. The cause may be genetic, environmental or unknown and can result in physical and/or mental impairment. Here is the latest research on birth defects.