Pattern and synchrony of gene expression among sympatric marine microbial populations

Proceedings of the National Academy of Sciences of the United States of America

Volumn 110, Issue 6, 2013, Pages

  Ottesen, Elizabeth A ^a   Young, Curtis R ^a   Eppley, John M ^a   Ryan, John P ^b   Chavez, Francisco P ^b   Scholin, Christopher A ^b   DeLong, Edward F ^a,c  

^a Departments of Civil and Environmental Engineering   (United States)

^b MONTEREY BAY AQUARIUM RESEARCH INSTITUTE   (United States)

^c MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

Autonomous sampling; Community ecology; Environmental microbiology; Metatranscriptomics; Microbial oceanography

Indexed keywords

RNA;

ARTICLE; CIRCADIAN RHYTHM; EURYARCHAEA; GAMMAPROTEOBACTERIA; GENE EXPRESSION PROFILING; HETEROTROPH; OSTREOCOCCUS; PELAGIBACTER; PICOPLANKTON; PRIORITY JOURNAL; RNA SEQUENCE; SYMPATRY; SYNECHOCOCCUS; TRANSCRIPTOMICS;

ARCHAEA; BACTERIA; BIODIVERSITY; CALIFORNIA; CIRCADIAN RHYTHM; ECOSYSTEM; GENE EXPRESSION PROFILING; METAGENOME; PHYLOGENY; PHYTOPLANKTON; PLANKTON; SEAWATER; SYNECHOCOCCUS; TRANSCRIPTOME; WATER MICROBIOLOGY;

EID: 84873455505     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1222099110     Document Type: Article

References (35)

1. Karl DM (2002) Nutrient dynamics in the deep blue sea. Trends Microbiol 10(9): 410-418.
2. Frias-Lopez J, et al. (2008) Microbial community gene expression in ocean surface waters. Proc Natl Acad Sci USA 105(10):3805-3810.
3. Gilbert JA, et al. (2008) Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. PLoS One 3(8):e3042.
4. Poretsky RS, et al. (2009) Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre. Environ Microbiol 11(6): 1358-1375.
5. Hewson I, Poretsky RS, Tripp HJ, Montoya JP, Zehr JP (2010) Spatial patterns and lightdriven variation of microbial population gene expression in surface waters of the oligotrophic open ocean. Environ Microbiol 12(7):1940-1956.
6. Ottesen EA, et al. (2011) Metatranscriptomic analysis of autonomously collected and preserved marine bacterioplankton. ISME J 5(12):1881-1895.
7. Marchetti A, et al. (2012) Comparative metatranscriptomics identifies molecular bases for the physiological responses of phytoplankton to varying iron availability. Proc Natl Acad Sci USA 109(6):E317-E325.
8. Gifford SM, Sharma S, Booth M, Moran MA (2012) Expression patterns reveal niche diversification in a marine microbial assemblage. ISME J, 10.1038/ismej.2012.96.
9. Martin AP, Zubkov MV, Burkill PH, Holland RJ (2005) Extreme spatial variability in marine picoplankton and its consequences for interpreting Eulerian time-series. Biol Lett 1(3):366-369.
10. Preston CM, et al. (2011) Underwater application of quantitative PCR on an ocean mooring. PLoS One 6(8):e22522.
11. Morris RM, et al. (2002) SAR11 clade dominates ocean surface bacterioplankton communities. Nature 420(6917):806-810.
12. Scanlan DJ, et al. (2009) Ecological genomics of marine picocyanobacteria. Microbiol Mol Biol Rev 73(2):249-299.
13. Demir-Hilton E, et al. (2011) Global distribution patterns of distinct clades of the photosynthetic picoeukaryote Ostreococcus. ISME J 5(7):1095-1107.
14. Dupont CL, et al. (2012) Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage. ISME J 6(6):1186-1199.
15. Iverson V, et al. (2012) Untangling genomes from metagenomes: Revealing an uncultured class of marine Euryarchaeota. Science 335(6068):587-590.
16. Li N, et al. (2010) Functional clustering of periodic transcriptional profiles through ARMA(p, q). PLoS One 5(4):e9894.
17. Ito H, et al. (2009) Cyanobacterial daily life with Kai-based circadian and diurnal genome-wide transcriptional control in Synechococcus elongatus. Proc Natl Acad Sci USA 106(33):14168-14173.
18. Monnier A, et al. (2010) Orchestrated transcription of biological processes in the marine picoeukaryote Ostreococcus exposed to light/dark cycles. BMC Genomics 11:192.
19. Binder BJ, Chisholm SW (1995) Cell cycle regulation in marine Synechococcus sp. strains. Appl Environ Microbiol 61(2):708-717.
20. Binder B (2000) Cell cycle regulation and the timing of chromosome replication in a marine Synechococcus (cyanobacteria) during light-and nitrogen-limited growth. J Phycol 36(1):120-126.
21. Sun J, et al. (2011) One carbon metabolism in SAR11 pelagic marine bacteria. PLoS One 6(8):e23973.
22. Keener J, Nomura M (1996) Regulation of ribosome synthesis. Escherichia coli and Salmonella: Cellular and Molecular Biology, eds Neidhardt FC, et al. (ASM Press, Washington, DC), 2nd Ed.
23. Fazio A, et al. (2008) Transcription factor control of growth rate dependent genes in Saccharomyces cerevisiae: A three factor design. BMC Genomics 9:341.
24. Hendrickson EL, et al. (2008) Global responses of Methanococcus maripaludis to specific nutrient limitations and growth rate. J Bacteriol 190(6):2198-2205.
25. Smith DP, et al. (2010) Transcriptional and translational regulatory responses to iron limitation in the globally distributed marine bacterium Candidatus pelagibacter ubique. PLoS One 5(5):e10487.
26. Giovannoni SJ, et al. (2005) Genome streamlining in a cosmopolitan oceanic bacterium. Science 309(5738):1242-1245.
27. Ng WL, Bassler BL (2009) Bacterial quorum-sensing network architectures. Annu Rev Genet 43:197-222.
28. Stewart FJ, Ottesen EA, DeLong EF (2010) Development and quantitative analyses of a universal rRNA-subtraction protocol for microbial metatranscriptomics. ISME J 4(7): 896-907.
29. Palenik B, et al. (2007) The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. Proc Natl Acad Sci USA 104(18):7705-7710.
30. Kanehisa M, Goto S (2000) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28(1):27-30.
31. Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M (2007) KAAS: An automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 35(Web Server issue):W182-W185.
32. Liu Z, Hsiao W, Cantarel BL, Drábek EF, Fraser-Liggett C (2011) Sparse distance-based learning for simultaneous multiclass classification and feature selection of metagenomic data. Bioinformatics 27(23):3242-3249.
33. Okansen J, et al. (2011) Vegan: Community Ecology Package, R Package Version 2.0-2. Available at http://cran.r-project.org/web//packages/vegan/index. html.
34. Team RDC (2012) R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, Vienna).
35. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate-a practical and powerful approach to multiple testing. J R Stat Soc Series B Stat Methodol 57(1): 289-300.