Preparation of microbial community cDNA for metatranscriptomic analysis in marine plankton

Methods in Enzymology

Volumn 531, Issue , 2013, Pages 187-218

  Stewart, Frank J ^a  

^a GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

Archaea; Bacteria; Metagenomics; Ocean; Ribosomal; RNA; RNA seq

Indexed keywords

BACTERIAL RNA; COMPLEMENTARY DNA; DNA POLYMERASE; MESSENGER RNA; RIBONUCLEASE; RIBOSOME RNA;

ADSORPTION; ARTICLE; BACTERIOPLANKTON; BIOMASS; DNA SYNTHESIS; ENVIRONMENTAL CHANGE; GENE EXPRESSION; HIGH THROUGHPUT SEQUENCING; MICROBIAL COMMUNITY; PLANKTON; PRECIPITATION; PRIORITY JOURNAL; RNA DEGRADATION; RNA EXTRACTION; RNA ISOLATION; SUBTRACTIVE HYBRIDIZATION;

ARCHAEA; BACTERIA; METAGENOMICS; OCEAN; RIBOSOMAL RNA; RNA-SEQ;

AQUATIC ORGANISMS; DNA, COMPLEMENTARY; GENE EXPRESSION PROFILING; METAGENOMICS; MICROBIAL CONSORTIA; PLANKTON;

EID: 84884561756     PISSN: 00766879     EISSN: 15577988     Source Type: Book Series    
DOI: 10.1016/B978-0-12-407863-5.00010-1     Document Type: Chapter

References (90)

1. N.M. Allewell, and A. Sama The effect of ammonium sulfate on the activity of ribonuclease A Biochimica et Biophysica Acta 341 1974 484 488
2. K. Anantharaman, J.A. Breier, C.S. Sheik, and G.J. Dick Evidence for hydrogen oxidation and metabolic plasticity in widespread deep-sea bacteria Proceedings of the National Academy of Sciences of the United States of America 110 2013 330 335
3. C.D. Armour, J.C. Castle, R. Chen, T. Babak, P. Loerch, and S. Jackson Digital transcriptome profiling using selective hexamer priming for cDNA synthesis Nature Methods 6 2009 647 649
4. D.S. Bachoon, F. Chen, and R.E. Hodson RNA recovery and detection of mRNA by RT-PCR from preserved prokaryotic samples FEMS Microbiology Letters 201 2001 127 132
5. T.C. Barnett, J.V. Bugrysheva, and J.R. Scott Role of mRNA stability in growth phase regulation of gene expression in the group A Streptococcus Journal of Bacteriology 189 2007 1866 1873
6. E.M. Brooks, L.G. Sheflin, and S.W. Spaulding Secondary structure in the 3′ UTR of EGF and the choice of reverse transcriptases affect the detection of message diversity by RT-PCR Biotechniques 19 1995 806 812
7. L.C. Burow, D. Woebken, I.P. Marshall, E.A. Lindquist, B.M. Bebout, and L. Prufert-Bebout Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics The ISME Journal 7 2013 817 829
8. D.E. Canfield, F.J. Stewart, B. Thamdrup, L. De Brabandere, T. Dalsgaard, and E.F. DeLong A cryptic sulfur cycle in oxygen-minimum zone waters off the Chilean Coast Science 330 2010 1375 1378
9. L.C. Carvalhais, P.G. Dennis, G.W. Tyson, and P.M. Schenk Application of metatranscriptomics to soil environments Journal of Microbiological Methods 91 2012 246 251
10. Z. Chen, and X. Duan Ribosomal RNA depletion for massively parallel bacterial RNA-sequencing applications Methods in Molecular Biology 733 2011 93 103
11. K.J. Coyne, S.M. Handy, E. Demir, E.B. Whereat, D.A. Hutchins, and K.J. Portune Improved quantitative real-time PCR assays for enumeration of harmful algal species in field samples using an exogenous DNA reference standard Limnology and Oceanography: Methods 3 2005 381 391
12. E.F. DeLong The microbial ocean from genomes to biomes Nature 459 2009 200 206
13. M.P. Deutscher Degradation of RNA in bacteria: Comparison of mRNA and stable RNA Nucleic Acids Research 34 2006 659 666
14. M. Dreyfus, and P. Régnier The poly(A) tail of mRNAs: Bodyguard in eukaryotes, scavenger in bacteria Cell 111 2002 611 613
15. J. Feike, K. Jürgens, J.T. Hollibaugh, S. Krüger, G. Jost, and M. Labrenz Measuring unbiased metatranscriptomics in suboxic waters of the central Baltic Sea using a new in situ fixation system The ISME Journal 6 2012 461 470
16. M.J. Filiatrault Progress in prokaryotic transcriptomics Current Opinion in Microbiology 14 2011 579 586
17. J. Frias-Lopez, Y. Shi, G.W. Tyson, M.L. Coleman, S.C. Schuster, and S.W. Chisholm Microbial community gene expression in ocean surface waters Proceedings of the National Academy of Sciences of the United States of America 105 2008 3805 3810
18. T. Fukatsu Acetone preservation: A practical technique for molecular analysis Molecular Ecology 8 1999 1935 1945
19. G. Giannoukos, D.M. Ciulla, K. Huang, B.J. Haas, J. Izard, and J.Z. Levin Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes Genome Biology 13 2012 R23
20. S.M. Gifford, S. Sharma, M. Booth, and M.A. Moran Expression patterns reveal niche diversification in a marine microbial assemblage The ISME Journal 7 2013 281 298
21. S.M. Gifford, S. Sharma, J.M. Rinta-Kanto, and M.A. Moran Quantitative analysis of a deeply sequenced marine microbial metatranscriptome The ISME Journal 5 2011 461 472
22. J.A. Gilbert, D. Field, Y. Huang, R. Edwards, W. Li, and P. Gilna Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities PLoS One 3 2008 e3042
23. J.A. Gilbert, D. Field, P. Swift, S. Thomas, D. Cummings, and B. Temperton The taxonomic and functional diversity of microbes at a temperate coastal site: A 'multi-omic' study of seasonal and diel temporal variation PLoS One 5 2010 e15545
24. E. Gorokhova Effects of preservation and storage of microcrustaceans in RNAlater on RNA and DNA degradation Limnology and Oceanography: Methods 3 2005 143 148
25. B.J. Haas, M. Chin, C. Nusbaum, B.W. Birren, and J. Livny How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes? BMC Genomics 13 2012 734
26. M.A. Hannah, H. Redestig, A. Leisse, and L. Willmitzer Global mRNA changes in microarray experiments Nature Biotechnology 26 2008 741 742
27. K.D. Hansen, S.E. Brenner, and S. Dudoit Biases in Illumina transcriptome sequencing caused by random hexamer priming Nucleic Acids Research 38 2010 e131
28. S. He, O. Wurtzel, K. Singh, J.L. Froula, S. Yilmaz, and S.G. Tringe Validation of two ribosomal RNA removal methods for microbial metatranscriptomics Nature Methods 7 2010 807 812
29. I. Hewson, R.S. Poretsky, R.A. Beinart, A.E. White, T. Shi, and S.R. Bench In situ transcriptomic analysis of the globally important keystone N2-fixing taxon Crocosphaera watsonii The ISME Journal 3 2009 618 631
30. I. Hewson, R.S. Poretsky, S.T. Dyhrman, B. Zielinski, A.E. White, and H.J. Tripp Microbial community gene expression within colonies of the diazotroph, Trichodesmium, from the Southwest Pacific Ocean The ISME Journal 3 2009 1286 1300
31. I. Hewson, R.S. Poretsky, H.J. Tripp, J.P. Montoya, and J.P. Zehr Spatial patterns and light-driven variation of microbial population gene expression in surface waters of the oligotrophic open ocean Environmental Microbiology 12 2010 1940 1956
32. J.T. Hollibaugh, S. Gifford, S. Sharma, N. Bano, and M.A. Moran Metatranscriptomic analysis of ammonia-oxidizing organisms in an estuarine bacterioplankton assemblage The ISME Journal 5 2011 866 878
33. J.L. Ingraham, O. Maaløe, and F.C. Neidhardt Growth of the bacterial cell 1983 Sinauer Associates Sunderland, MA, USA
34. K.H. Kim, and J.W. Bae Amplification methods bias metagenomic libraries of uncultured single-stranded and double-stranded DNA viruses Applied and Environmental Microbiology 77 2011 7663 7668
35. S.M. Kristoffersen, C. Haase, M.R. Weil, K.D. Passalacqua, F. Niazi, and S.K. Hutchison Global mRNA decay analysis at single nucleotide resolution reveals segmental and positional degradation patterns in a Gram-positive bacterium Genome Biology 13 2012 R30
36. P. Kukutla, M. Steritz, and J. Xu Depletion of ribosomal RNA for mosquito gut metagenomic RNA-seq Journal of Visualized Experiments 74 2013 e50093
37. Lader, E. (1998). Methods and reagents for preserving RNA in cell and tissue samples. U.S. Patent 6204375, filed July 31, 1998, issued March 20, 2001.
38. P. Lam, M.M. Jensen, G. Lavik, D.F. McGinnis, B. Müller, and C.J. Schubert Linking crenarchaeal and bacterial nitrification to anammox in the Black Sea Proceedings of the National Academy of Sciences of the United States of America 104 2007 7104 7109
39. S. Lee, and P.F. Kemp Single-cell RNA content of natural marine planktonic bacteria measured by hybridization with multiple 16S rRNA-targeted fluorescent probes Limnology and Oceanography 39 1994 869 879
40. R.A. Lesniewski, S. Jain, K. Anantharaman, P.D. Schloss, and G.J. Dick The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs The ISME Journal 6 2012 2257 2268
41. Y.W. Lim, R. Schmieder, M. Haynes, D. Willner, M. Furlan, and M. Youle Metagenomics and metatranscriptomics: Windows on CF-associated viral and microbial communities Journal of Cystic Fibrosis 12 2012 154 164
42. S. Lin, H. Zhang, Y. Zhuang, B. Tran, and J. Gill Spliced leader-based metatranscriptomic analyses lead to recognition of hidden genomic features in dinoflagellates Proceedings of the National Academy of Sciences of the United States of America 107 2010 20033 20038
43. L. Liu, Y. Li, S. Li, N. Hu, Y. He, and R. Pong Comparison of next-generation sequencing systems Journal of Biomedicine and Biotechnology 2012 2012 251364
44. C. Luo, D. Tsementzi, N. Kyrpides, T. Read, and K.T. Konstantinidis Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample PLoS One 7 2012 e30087
45. J. McCarren, J.W. Becker, D.J. Repeta, Y. Shi, C.R. Young, and R.R. Malmstrom Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea Proceedings of the National Academy of Sciences of the United States of America 107 2010 16420 16427
46. K.C. McGrath, S.R. Thomas-Hall, C.T. Cheng, L. Leo, A. Alexa, and S. Schmidt Isolation and analysis of mRNA from environmental microbial communities Journal of Microbiological Methods 75 2008 172 176
47. M.A. Moran Metatranscriptomics: Eavesdropping on complex microbial communities Microbe 4 2009 329 335
48. M.A. Moran, B. Satinsky, S.M. Gifford, H. Luo, A. Rivers, and L.K. Chan Sizing up metatranscriptomics The ISME Journal 7 2013 237 243
49. X. Mou, M. Vila-Costa, S. Sun, W. Zhao, S. Sharma, and M.A. Moran Metatranscriptomic signature of exogenous polyamine utilization by coastal bacterioplankton Environmental Microbiology Reports 3 2011 798 806
50. G.L. Mutter, D. Zahrieh, C. Liu, D. Neuberg, D. Finkelstein, and H.E. Baker Comparison of frozen and RNALater solid tissue storage methods for use in RNA expression microarrays BMC Genomics 5 2004 88
51. D.K. Nam, S. Lee, G. Zhou, X. Cao, C. Wang, and T. Clark Oligo(dT) primer generates a high frequency of truncated cDNAs through internal poly(A) priming during reverse transcription Proceedings of the National Academy of Sciences of the United States of America 99 2002 6152 6156
52. F.C. Neidhardt, and H.E. Umbarger Chemical composition of Escherichia coli F.C. Neidhardt, Escherichia coli and Salmonella: Cellular and molecular biology 1996 ASM Press Washington, DC 13 17
53. E.A. Ottesen, R. Marin 3rd., C.M. Preston, C.R. Young, J.P. Ryan, and C.A. Scholin Metatranscriptomic analysis of autonomously collected and preserved marine bacterioplankton The ISME Journal 5 2011 1881 1895
54. E.A. Ottesen, C.R. Young, J.M. Eppley, J.P. Ryan, F.P. Chavez, and C.A. Scholin Pattern and synchrony of gene expression among sympatric marine microbial populations Proceedings of the National Academy of Sciences of the United States of America 110 2013 E488 E497
55. D. Parkhomchuk, T. Borodina, V. Amstislavskiy, M. Banaru, L. Hallen, and S. Krobitsch Transcriptome analysis by strand-specific sequencing of complementary DNA Nucleic Acids Research 37 2009 e123
56. C. Peano, A. Pietrelli, C. Consolandi, E. Rossi, L. Petiti, and L. Tagliabue An efficient rRNA removal method for RNA sequencing in GC-rich bacteria Microbial Informatics and Experimentation 3 2013 1
57. R.S. Poretsky, N. Bano, A. Buchan, G. LeCleir, J. Kleikemper, and M. Pickering Analysis of microbial gene transcripts in environmental samples Applied and Environmental Microbiology 71 2005 4121 4126
58. R.S. Poretsky, S. Gifford, J. Rinta-Kanto, M. Vila-Costa, and M.A. Moran Analyzing gene expression from marine microbial communities using environmental transcriptomics Journal of Visualized Experiments 24 2009 e1086
59. R.S. Poretsky, I. Hewson, S. Sun, A.E. Allen, J.P. Zehr, and M.A. Moran Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre Environmental Microbiology 11 2009 1358 1375
60. R.S. Poretsky, S. Sun, X. Mou, and M.A. Moran Transporter genes expressed by coastal bacterioplankton in response to dissolved organic carbon Environmental Microbiology 12 2010 616 627
61. M.A. Quail, M. Smith, P. Coupland, T.D. Otto, S.R. Harris, and T.R. Connor A tale of three next generation sequencing platforms: Comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers BMC Genomics 13 2012 341
62. R. Raghavan, D.B. Sloan, and H. Ochman Antisense transcription is pervasive but rarely conserved in enteric bacteria mBio 3 2012 e00156-12
63. J.M. Rinta-Kanto, S. Sun, S. Sharma, R.P. Kiene, and M.A. Moran Bacterial community transcription patterns during a marine phytoplankton bloom Environmental Microbiology 14 2012 228 239
64. A.J. Rissanen, E. Kurhela, T. Aho, T. Oittinen, and M. Tiirola Storage of environmental samples for guaranteeing nucleic acid yields for molecular microbiological studies Applied Microbiology and Biotechnology 88 2010 977 984
65. A. Roberts, C. Trapnell, J. Donaghey, J.L. Rinn, and L. Pachter Improving RNA-Seq expression estimates by correcting for fragment bias Genome Biology 12 2011 R22
66. H. Roume, E.E. Muller, T. Cordes, J. Renaut, K. Hiller, and P. Wilmes A biomolecular isolation framework for eco-systems biology The ISME Journal 7 2013 110 121
67. J.G. Sanders, R.A. Beinart, F.J. Stewart, E.F. DeLong, and P.R. Girguis Metatranscriptomics reveal differences in in situ energy and nitrogen metabolism among hydrothermal vent snail symbionts The ISME Journal 7 2013 1556 1567 10.1038/ismej.2013.45
68. N. Sarkar Polyadenylation of mRNA in prokaryotes Annual Review of Biochemistry 66 1997 173 197
69. C. Scholin, G. Doucette, S. Jensen, B. Roman, D. Pargett, and R. Marin Remote detection of marine microbes, small invertebrates, harmful algae, and biotoxins using the Environmental Sample Processor (ESP) Oceanography 22 2009 158 167
70. D.W. Selinger, R.M. Saxena, K.J. Cheung, G.M. Church, and C. Rosenow Global RNA half-life analysis in Escherichia coli reveals positional patterns of transcript degradation Genome Research 13 2003 216 223
71. C.M. Sharma, S. Hoffmann, F. Darfeuille, J. Reignier, S. Findeiss, and A. Sittka The primary transcriptome of the major human pathogen Helicobacter pylori Nature 464 2010 250 255
72. Y. Shi, J. McCarren, and E.F. DeLong Transcriptional responses of surface water marine microbial assemblages to deep-sea water amendment Environmental Microbiology 14 2012 191 206
73. Y. Shi, G.W. Tyson, and E.F. DeLong Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column Nature 459 2009 266 269
74. Y. Shi, G.W. Tyson, J.M. Eppley, and E.F. DeLong Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean The ISME Journal 5 2011 999 1013
75. R.L. Simister, S. Schmitt, and M.W. Taylor Evaluating methods for the preservation and extraction of DNA and RNA for analysis of microbial communities in marine sponges Journal of Experimental Marine Biology and Ecology 397 2011 38 43
76. C. Steglich, D. Lindell, M. Futschik, T. Rector, R. Steen, and S.W. Chisholm Short RNA half-lives in the slow-growing marine cyanobacterium Prochlorococcus Genome Biology 11 2010 R54
77. F.J. Stewart, T. Dalsgaard, B. Thamdrup, N.P. Revsbech, O. Ulloa, and D.E. Canfield Experimental incubations elicit profound changes in community transcription in OMZ bacterioplankton PLoS One 7 2012 e37118
78. F.J. Stewart, E.A. Ottesen, and E.F. DeLong Development and quantitative analyses of a universal rRNA-subtraction protocol for microbial metatranscriptomics The ISME Journal 4 2010 896 907
79. F.J. Stewart, A.K. Sharma, J.A. Bryant, J.M. Eppley, and E.F. DeLong Community transcriptomics reveals universal patterns of protein sequence conservation in natural microbial communities Genome Biology 12 2011 R26
80. F.J. Stewart, O. Ulloa, and E.F. DeLong Microbial metatranscriptomics in a permanent marine oxygen minimum zone Environmental Microbiology 14 2012 23 40
81. E. Strady, C. Pohl, E.V. Yakushev, S. Krüger, and U. Hennings PUMP-CTD-System for trace metal sampling with a high vertical resolution. A test in the Gotland Basin, Baltic Sea Chemosphere 70 2008 1309 1319
82. Y. Taniguchi, P.J. Choi, G.W. Li, H. Chen, M. Babu, and J. Hearn Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells Science 329 2010 533 538
83. T. Urich, A. Lanzén, J. Qi, D.H. Huson, C. Schleper, and S.C. Schuster Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome PLoS One 3 2008 e2527
84. V.A. Vandernoot, S.A. Langevin, O.D. Solberg, P.D. Lane, D.J. Curtis, and Z.W. Bent cDNA normalization by hydroxyapatite chromatography to enrich transcriptome diversity in RNA-seq applications Biotechniques 53 2012 373 380
85. M. Vila-Costa, J.M. Rinta-Kanto, S. Sun, S. Sharma, R. Poretsky, and M.A. Moran Transcriptomic analysis of a marine bacterial community enriched with dimethylsulfoniopropionate The ISME Journal 4 2010 1410 1420
86. V.F. Wendisch, D.P. Zimmer, A. Khodursky, B. Peter, N. Cozzarelli, and S. Kustu Isolation of Escherichia coli mRNA and comparison of expression using mRNA and total RNA on DNA microarrays Analytical Biochemistry 290 2001 205 213
87. C. Wurzbacher, I. Salka, and H.P. Grossart Environmental actinorhodopsin expression revealed by a new in situ filtration and fixation sampler Environmental Microbiology Reports 4 2012 491 497
88. X. Xiong, D.N. Frank, C.E. Robertson, S.S. Hung, J. Markle, and A.J. Canty Generation and analysis of a mouse intestinal metatranscriptome through Illumina based RNA-sequencing PLoS One 7 2012 e36009
89. H. Yi, Y.J. Cho, S. Won, J.E. Lee, H. Jin Yu, and S. Kim Duplex-specific nuclease efficiently removes rRNA for prokaryotic RNA-seq Nucleic Acids Research 39 2011 e140
90. S. Yilmaz, M. Allgaier, and P. Hugenholtz Multiple displacement amplification compromises quantitative analysis of metagenomes Nature Methods 7 2010 943 944