Optimization of whole-transcriptome amplification from low cell density deep-sea microbial samples for metatranscriptomic analysis

Journal of Microbiological Methods

Volumn 84, Issue 1, 2011, Pages 88-93

  Wu, Jieying ^a   Gao, Weimin ^a   Zhang, Weiwen ^a   Meldrum, Deirdre R ^a  

^a ARIZONA STATE UNIVERSITY   (United States)

Author keywords

Amplification; Deep sea microbial samples; Whole transcriptome

Indexed keywords

COMPLEMENTARY DNA; DOUBLE STRANDED DNA; SINGLE STRANDED DNA; TITANIUM; TRANSCRIPTOME;

ARTICLE; BACTERIAL MEMBRANE; BACTERIUM ISOLATION; BIOLOGICAL MONITORING; BIOSENSOR; CELL DENSITY; CONTROLLED STUDY; DEEP SEA SPECIES; INTERMETHOD COMPARISON; METAGENOMICS; MICROBIAL DIVERSITY; MICROBIAL POPULATION DYNAMICS; MOLECULAR CLONING; MOLECULAR LIBRARY; NONHUMAN; NUCLEIC ACID AMPLIFICATION; NUCLEIC ACID DATABASE; OCEANOGRAPHY; PRIORITY JOURNAL; PROCESS DEVELOPMENT; PROCESS OPTIMIZATION; PYROSEQUENCING; QUALITY CONTROL; TRANSCRIPTOMICS;

GENE EXPRESSION PROFILING; METAGENOMICS; NUCLEIC ACID AMPLIFICATION TECHNIQUES; SEAWATER;

EID: 78650195187     PISSN: 01677012     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mimet.2010.10.018     Document Type: Article

References (36)

1. Berthet N., Reinhardt A.K., Leclercq I., van Ooyen S., Batéjat C., Dickinson P., et al. Phi29 polymerase based random amplification of viral RNA as an alternative to random RT-PCR. BMC Mol. Biol. 2008, 9:77.
2. Boehme K., Simon S., Mueller S.O. Gene expression profiling in Ishikawa cells: a fingerprint for estrogen active compounds. Toxicol. Appl. Pharmacol. 2009, 236:85-96.
3. Boysen-Ennen E., Hagen W., Hubold G., Piatkowski U. Zooplankton biomass in the ice-covered Weddell Sea, Antarctica. Mar. Biol. 1991, 111:227-235.
4. Broemeling D.J., Pel J., Gunn D.C., Mai L., Thompson J.D., Poon H., et al. An instrument for automated purification of nucleic acids from contaminated forensic samples. JALA (Charlottesville, Va.) 2008, 13:40-48.
5. Burns D.A., Mitchell J.S. Further examples of the dinoflagellate genus Ceratium from New Zealand coastal waters. NZ J. Mar. Freshw. Res. 1982, 16:57.
6. Chistoserdova L. Recent progress and new challenges in metagenomics for biotechnology. Biotechnol. Lett. 2010, 32:1351-1359.
7. Clement-Ziza M., Gentien D., Lyonnet S., Thiery J.-P., Besmond C., Decraene C. Evaluation of methods for amplification of picogram amounts of total RNA for whole genome expression profiling. BMC Genomics 2009, 10:246.
8. Demeke T., Jenkins G.R. Influence of DNA extraction methods, PCR inhibitors and quantification methods on real-time PCR assay of biotechnology-derived traits. Anal. Bioanal. Chem. 2010, 396:1977-1990.
9. Frias-Lopez J., Shi Y., Tyson G.W., Coleman M.L., Schuster S.C., Chisholm S.W., et al. Microbial community gene expression in ocean surface waters. Proc. Natl Acad. Sci. USA 2008, 105:3805-3810.
10. Frost B.W. Calanus marshallae, a new species of calanoid copepod closely allied to the sibling species C. finmarchicus and C. glacialis. Mar. Biol. 1974, 26:77-99.
11. Gailhard I., Gros Ph., Durbec J., Beliaeff B., Belin C., Nézan E., et al. Variability patterns of microphytoplankton communities along the French coasts. Mar. Ecol. Prog. Ser. 2002, 242:39-50.
12. Gilbert J.A., Field D., Huang Y., Edwards R., Li W., Gilna P., et al. Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. PLoS ONE 2008, 3:e3042.
13. Gonzalez J.M., Covert J.S., Whitman W.B., Henriksen J.R., Mayer F., Scharf B., et al. Silicibacter pomeroyi sp. nov. and Roseovarius nubinhibens sp. nov., dimethylsulfoniopropionate-demethylating bacteria from marine environments. Int. J. Syst. Evol. Microbiol. 2003, 53:1261-1269.
14. Greuet C. Ultrastructural organization of the ocelloide of Nematodinium. Phylogenetic aspect of the evolution of Warnowiidae Lindemann dinoflagellates photoreceptor. Cytobiologie 1978, 17:114-136.
15. Hwang J.-S., Souissi S., Tseng L.-C., Seuront L., Schmitt F.G., Fang L.-S., et al. A 5-year study of the influence of the northeast and southwest monsoons on copepod assemblages in the boundary coastal waters between the East China Sea and the Taiwan Strait. J. Plankton Res. 2007, 29:97-116.
16. Imhoff J. True marine and halophilic anoxygenic phototrophic bacteria. Arch. Microbiol. 2001, 176:243-254.
17. Jeong H.G., Suh H.-L., Yoon Y.H., Soh H.Y. Redescription of Pontella species (Calanoida, Pontellidae) from Korean waters, with notes on their spatio-temporal distribution. Ocean Sci. J. 2008, 43:209-222.
18. Katz M.E., Tjalsma R.C., Miller K.G. Oligocene bathyal to abyssal benthic foraminifera of the Atlantic Ocean. Micropaleontology 2003, 49:1-45.
19. Kimor B., Gordon N., Neori A. Symbiotic associations among the microplankton in oligotrophic marine environments, with special reference to the Gulf of Aqaba, Red Sea. J. Plankton Res. 1992, 14:1217-1231.
20. Klimpel S., Palm H.W., Rückert S., Piatkowski U. The life cycle of Anisakis simplex in the Norwegian Deep (northern North Sea). Parasitol. Res. 2004, 94:1-9.
21. Kosobokova K.N., Hanssen H., Hirche H.-J., Knickmeier K. Composition and distribution of zooplankton in the Laptev Sea and adjacent Nansen Basin during summer, 1993. Polar Biol. 1997, 19:63-76.
22. Madhupratap M., Haridas P. Zooplankton, especially calanoid copepods, in the upper 1000m of the south-east Arabian Sea. J. Plankton Res. 1990, 12:305-321.
23. McGrath K.C., Thomas-Hall S.R., Cheng C.T., Leo L., Alexa A., Schmidt S., et al. Isolation and analysis of mRNA from environmental microbial communities. J. Microbiol. Meth. 2008, 75:172-176.
24. Meyer F., Paarmann D., D'Souza M., Olson R., Glass E.M., Kubal M., et al. The metagenomics RAST server-a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinform. 2008, 9:386.
25. Mincer T.J., Church M.J., Taylor L.T., Preston C., Karl D.M., DeLong E.F. Quantitative distribution of presumptive archaeal and bacterial nitrifiers in Monterey Bay and the North Pacific Subtropical Gyre. Environ. Microbiol. 2007, 9:1162-1175.
26. Moran M.A. Metatranscriptomics: eavesdropping on complex microbial communities. Microbe Mag. 2009, 4:329-335.
27. Poretsky R.S., Gifford S., Rinta-Kanto J., Vila-Costa M., Moran M.A. Analyzing gene expression from marine microbial communities using environmental transcriptomics. J. Vis. Exp. 2009, 24.
28. Schnitker D. Quaternary deep-sea benthic foraminifers and bottom water masses. Annu. Rev. Earth Planet. Sci. 1980, 8:343-370.
29. Shi Y., Tyson G.W., DeLong E.F. Metatranscriptomics reveals unique microbial small RNAs in the ocean/'s water column. Nature 2009, 459:266-269.
30. Sorensen K.B., Lauer A., Teske A. Archaeal phylotypes in a metal-rich and low-activity deep subsurface sediment of the Peru Basin, ODP Leg 201, Site 1231. Geobiology 2004, 2:151-161.
31. Takai K., Gamo T., Tsunogai U., Nakayama N., Hirayama H., Nealson K.H., et al. Geochemical and microbiological evidence for a hydrogen-based, hyperthermophilic subsurface lithoautotrophic microbial ecosystem (HyperSLiME) beneath an active deep-sea hydrothermal field. Extremophiles 2004, 8:269-282.
32. Tseng L.-C., Dahms H.-U., Chen Q.-C., Hwang J.-S. Copepod assemblages of the Northern South China Sea. Crustaceana 2008, 81:1-22.
33. Urich T., Lanzén A., Qi J., Huson D.H., Schleper C., Schuster S.C. Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome. PLoS ONE 2008, 3:e2527.
34. Van La M., Barbry P., Raoult D., Renesto P. Molecular basis of Tropheryma whipplei doxycycline susceptibility examined by transcriptional profiling. J. Antimicrob. Chemother. 2007, 59:370-377.
35. Vila-Costa M., Rinta-Kanto J.M., Sun S., Sharma S., Poretsky R., Moran M.A. Transcriptomic analysis of a marine bacterial community enriched with dimethyl-sulfoniopropionate. ISME J. 2010, 4:1410-1420.
36. Wei Y., Yu M. Phytoplanktonic desmids community in Donghu Lake, Wuhan, China. Chin. J. Oceanol. Limnol. 2005, 23:91-97.