Chapter 27
Detection of Large Numbers of Novel Sequences in the Metatranscriptomes of Complex Marine Microbial Communities
Jack A. Gilbert,
Dawn Field,
Ying Huang,
Robert A. Edwards,
Weizhong Li,
Paul Gilna,
Ian Joint,
Jack A. Gilbert
Plymouth Marine Laboratory, Plymouth, United Kingdom
Search for more papers by this authorDawn Field
NERC Centre for Ecology and Hydrology, Oxford, United Kingdom
Search for more papers by this authorYing Huang
University of California, San Diego, La Jolla, California, USA
Search for more papers by this authorRobert A. Edwards
San Diego State University, San Diego, California; Argonne National Laboratory, Argonne, Illinois, USA
Search for more papers by this authorWeizhong Li
University of California, San Diego, La Jolla, California, USA
Search for more papers by this authorPaul Gilna
University of California, San Diego, La Jolla, California, USA
Search for more papers by this authorJack A. Gilbert,
Dawn Field,
Ying Huang,
Robert A. Edwards,
Weizhong Li,
Paul Gilna,
Ian Joint,
Jack A. Gilbert
Plymouth Marine Laboratory, Plymouth, United Kingdom
Search for more papers by this authorDawn Field
NERC Centre for Ecology and Hydrology, Oxford, United Kingdom
Search for more papers by this authorYing Huang
University of California, San Diego, La Jolla, California, USA
Search for more papers by this authorRobert A. Edwards
San Diego State University, San Diego, California; Argonne National Laboratory, Argonne, Illinois, USA
Search for more papers by this authorWeizhong Li
University of California, San Diego, La Jolla, California, USA
Search for more papers by this authorPaul Gilna
University of California, San Diego, La Jolla, California, USA
Search for more papers by this authorBook Editor(s):Frans J. de Bruijn,
Frans J. de Bruijn
Laboratory of Plant Micro-organism Interaction, CNRS-INRA, Castanet Tolosan, France
Search for more papers by this authorSummary
This chapter contains sections titled:
-
Introduction
-
Methods
-
Results and Discussion
-
Summary
-
Internet Resources
-
References
INTERNET RESOURCES
- University of Liverpool (http://www.liv.ac.uk/agf/)
- GEO (http://www.ncbi.nlm.nih.gov/geo/)
- Refseq-(ftp://ftp.ncbi.nih.gov/refseq/release/releasestatistics/RefSeqrelease27.01062008.stats.txt)
- PFAM database (http://PFAM.sanger.ac.uk/)
- TIGRfam database (http://www.tigr.org/TIGRFAMs/)
- COG database (http://www.ncbi.nlm.nih.gov/COG/)
- Probes (http://probes.pw.usda.gov/cgi-bin/batchprimer3/batchprimer3.cgi)
- Primers (http://nebc.nox.ac.uk/nebcfs/public/Joint/metatranscript_primers.xls)
- Metagenome Rapid Annotation using Subsystem Technology (http://metagenomics.theseed.org)
- REFERENCES
- Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, et al. 2008. The RAST server: Rapid annotations using subsystems technology. BMC Genomics 9: 75.
- DeLong EF, Preston CM, Mincer T, Rich V, Hallam SJ, et al. 2006. Community genomics among stratified microbial assemblages in the ocean's interior. Science 311: 496–503.
- Francois P, Garzoni C, Bento M, Schrenzel J. 2007. Comparison of amplification methods for transcriptomic analyses of low abundance prokaryotic RNA sources. J Microbiol. Methods 68: 385–391.
- Frias-Lopez J, Shi Y, Tyson GW, Coleman ML, Schuster SC, et al. 2008. Microbial community gene expression in ocean surface waters. Proc. Natl. Acad. Sci. USA 105: 3805–3810.
- Gilbert JA, Field D, Huang Y, Edwards R, Li W, et al. 2008. Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. PLoS ONE 3(8): e3042.
- Gilbert JA, Thomas S, Cooley N, Kulakova A, Field D, et al. 2009. Potential for phosphonoacetate utilisation by marine bacteria in temperate coastal waters. Environ. Microb. 11(1): 111–125.
- Griffiths, RI, Whiteley AS, O'Donnell AG, Bailey MJ. 2000. Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition. Appl. Environ. Microbiol. 66: 5488–5491.
- Handelsman J, Tiedje J, Alvarez-Cohen L, Ashburner M, Cann IKO, et al. 2007. The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet. Washington, DC: The National Academies Press.
- Leininger S, Urich T, Schloter M, Schwark L, Qi J, et al. 2006. Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442: 806–809.
- Li, Godzik A. 2006. Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22: 1658–1659.
- Lipman DJ, Souvorov A, Koonin EV, Panchenko AR, Tatusova TA. 2002. The relationship of protein conservation and sequence length. BMC Evol. Biol. 2: 20.
- Neufeld JD, Schäfer H, Cox MJ, Boden R, McDonald IR, et al. 2007. Stable-isotope probing implicates Methylophaga spp and novel Gammaproteobacteria in marine methanol and methylamine metabolism. ISME J. 1: 480–491.
- Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, et al. 2005. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 33: 5691–5702.
- Poretsky RS, Bano N, Buchan A, LeCleir G, Kleikemper J, et al. 2005. Analysis of microbial gene transcripts in environmental samples. Appl. Environ. Microbiol. 71: 4121–4126.
- Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, et al. 2007. The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol. 5: 398–431.
- Seshadri R, Kravitz SA, Smarr L, Gilna P, Frazier M. 2007. CAMERA: A community resource for metagenomics. PLoS Biol. 5: e75.
- Urich T, Lanzén A, Qi J, Huson DH, Schleper C, et al. 2008. Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome. PLoS ONE 3: e2527.
- Wilson GA, Feil EJ, Lilley AK, Field D. 2007. Large-scale comparative genomic ranking of taxonomically restricted genes (TRGs) in bacterial and archaeal genomes. PLoS ONE 2(3): e324.
- Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, et al. 2007. The Sorcerer II Global Ocean Sampling expedition: Expanding the universe of protein families. PLoS Biol. 5: 432–466.
- Zhang K, Martiny AC, Reppas NB, Barry KW, Malek J, et al. 2006. Sequencing genomes from single cells by polymerase cloning. Nat. Biotech. 24: 680–686.
