Chapter 30
A Targeted Metagenomic Approach to Determine the “Population Genome” of Marine Synechococcus
Sophie Mazard, Martin Ostrowski,
Laurence Garczarek,
David J. Scanlan,
Martin Ostrowski
University of Warwick, Coventry, United Kingdom
Search for more papers by this authorLaurence Garczarek
University of Paris 6 and CNRS, Roscoff, France
Search for more papers by this authorDavid J. Scanlan
University of Paris 6 and CNRS, Roscoff, France
Search for more papers by this authorSophie Mazard, Martin Ostrowski,
Laurence Garczarek,
David J. Scanlan,
Martin Ostrowski
University of Warwick, Coventry, United Kingdom
Search for more papers by this authorLaurence Garczarek
University of Paris 6 and CNRS, Roscoff, France
Search for more papers by this authorDavid J. Scanlan
University of Paris 6 and CNRS, Roscoff, France
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:
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Introduction
-
Materials and Methods
-
Results and Discussion
-
Conclusions
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Internet Resources
-
References
INTERNET RESOURCES
- Mothur software (http://schloss.micro.umass.edu/wiki/Main_Page)
- Metagenome Rapid Annotation using Subsystem Technology MG-RAST (http://metagenomics.nmpdr.org/)
- REFERENCES
- Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25: 3389–3402.
- Audic S, Lescot M, Claverie JM, Scholz HC. 2009. Brucella microti : The genome sequence of an emerging pathogen. BMC Genomics 10: 352.
- Baumdicker F, Pfaffelhuber P, Hess WR. 2011. The pan- and supragenome of marine picocyanobacteria and definition of their core genome. Mol. Biol. Evol. submitted.
- Biers EJ, Sun S, Howard EC. 2009. Prokaryotic genomes and diversity in surface ocean waters: interrogating the global ocean sampling metagenome. Appl. Environ. Microbiol. 75: 2221–2229.
- Cuadros-Orellana S, Martin-Cuadrado AB, Legault B, D'Auria G, Zhaxybayeva O, Papke RT, Rodriguez-Valera F. 2007. Genomic plasticity in prokaryotes: The case of the square haloarchaeon. ISME J. 1: 235–245.
- Deyde VM, Gubareva LV. 2009. Influenza genome analysis using pyrosequencing method: Current applications for a moving target. Expert Rev. Mol. Diagn. 5: 493–509.
- Dufresne A, Ostrowski M, Scanlan DJ, Garczarek L, Mazard S, et al. 2008. Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria. Genome Biol. 9: R90.
- Fuller NJ, Marie D, Partensky F, Vaulot D, Post AF, Scanlan DJ. 2003. Clade-specific 16S ribosomal DNA oligonucleotides reveal the predominance of a single marine Synechococcus clade throughout a stratified water column in the Red Sea. Appl. Environ. Microbiol. 69: 2430–2443.
- Gioanoulis TA, Raes J, Patel PV, Bjornson R, Korbel JO, et al. 2009. Quantifying environmental adaptation of metabolic pathways in metagenomics. Proc. Natl. Acad. Sci. USA 106: 1374–1379.
- Gilbert JA, Field D, Huang Y, Edwards R, Li W, Gilna P, Joint I. 2008. Detection of large numbers of novel sequences in the meta-transcriptomes of complex marine microbial communities. PLoS ONE 3: e3042.
- Ishoey T, Woyke T, Stepanauskas R, Novotny M, Lasken RS. 2008. Genomic sequencing of single microbial cells from environmental samples. Curr. Opin. Microbiol. 3: 198–204.
- Mazard S, Ostrowski M, Partensky F, Scanlan DJ. 2011. Multi-locus sequence analysis, taxonomic resolution and biogeography of marine Synechococcus. Env. Microbiol. (submitted).
- McCarren J, Brahamsha B. 2007. SwmB, a 1.12-megadalton protein that is required for nonflagellar swimming motility in Synechococcus. J. Bacteriol. 189: 1158–1162.
- Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, et al. 2008. The Metagenomics RAST server—A public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9: 386.
- Palenik, B, Ren QH, Dupont CL, Myers GS, Heidelberg JF, et al. 2006. Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment. Proc. Natl. Acad. Sci. USA 103: 13555–13559.
- Palenik B, Ren Q, Tai V, Paulsen IT. 2009. Coastal Synechococcus metagenome reveals major roles for horizontal gene transfer and plasmids in population diversity. Environ. Microbiol. 11: 349–359.
- Poretsky RS, Hewson I, Sun S, Allen AE, Zehr JP, Moran MA. 2009. Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre. Environ. Microbiol. 11: 1358–1375.
- Quince C, Curtis TP, Sloan WT. 2008. The rational exploration of microbial diversity. ISME J. 2: 997–1006.
- Rocap G, Distel DL, Waterbury JB, Chisholm SW. 2002. Resolution of Prochlorococcus and Synechococcus ecotypes by using 16S–23S ribosomal DNA internal transcribed spacer sequences. Appl. Environ. Microbiol. 68: 1180–1191.
- Rothberg JM, Leamon JH. 2008. The development and impact of 454 sequencing. Nat. Biotechnol. 26: 1117–1124.
- 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: e77.
- Scanlan DJ. 2003. Physiological diversity and niche adaptation in marine Synechococcus. Adv. Microb. Physiol. 47: 1–64.
- Scanlan DJ, Ostrowski M, Mazard S, Dufresne A, Garczarek L, et al. 2009. Ecological genomics of marine picocyanobacteria. Micro-biol. Mol. Biol. Rev. 73: 249–299.
- Shi, Y, Tyson GW, Delong EF. 2009. Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column. Nature 459: 266–272.
- Suzuki, M, Rappe MS, Giovannoni SJ. 1998. Kinetic bias in estimates of coastal picoplankton community structure obtained by measurements of small-subunit rRNA gene PCR amplicon length heterogeneity. Appl. Environ. Microbiol. 64: 4522–4529.
- Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, et al. 2004. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428: 37–43.
- Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, et al. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66–74.
- Woyke T, Xie G, Copeland A, González JM, Han C, et al. 2009. Assembling the marine metagenome, one cell at a time. PLoS ONE 4: e5299.
- Zwirglmaier, K, Jardillier L, Ostrowski M, Mazard S, Garczarek L, et al. 2008. Global phylogeography of marine Synechococcus and Prochlorococcus reveals a distinct partitioning of lineages among oceanic biomes. Environ. Microbiol. 10: 147–161.
