Methods in Metagenomic DNA, RNA, and Protein Isolation from Soil

Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats

Volumn , Issue , 2011, Pages 93-107

  Rajesh, T ^a   Rajendhran, J ^a   Pushpam, P Lavanya ^a   Gunasekaran, P ^a  

^a MADURAI KAMARAJ UNIVERSITY   (India)

Author keywords

Metagenomic DNA, RNA, isolation; Metatranscriptomics; Soil RNA isolation

Indexed keywords

EID: 84860302760     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9781118010549.ch10     Document Type: Chapter

References (74)

1. Arbeli Z, Fuentes CL. 2007. Improved purification and PCR amplification of DNA from environmental samples. FEMS Microbiol. Lett. 272:269-275.
2. Benndorf D, Balcke GU, Harms H, Von Bergen M. 2007. Functional metaproteome analysis of protein extracts from contaminated soil and groundwater. ISME J. 1:224-234.
3. Bernardi G. 1971. Chromatography of nucleic acids on hydroxyapatite columns. Methods Enzymol. 21:95-139.
4. Braid MD, Daniels LM, Kitts CL. 2003. Removal of PCR inhibitors from soil DNA by chemical flocculation. J. Microbiol. Methods 52:389-393.
5. Burgmann H, Pesaro M, Widmer F, Zeyer J. 2001. A strategy for optimizing quality and quantity of DNA extracted from soil. J. Microbiol. Methods 45:17-20.
6. Burgmann H, Widmer F, Sigler WV, Zeyer J. 2003. mRNA extraction and reverse transcription-PCR protocol for detection of nifH gene expression by Azotobacter vinelandii in soil. Appl. Environ. Microbiol. 69:1928-1935.
7. Chandler DP, Brockman FJ, Fredrickson JK. 1997. Effect of PCR template concentration on the composition and distribution of total community 16S rDNA clone libraries. Mol. Ecol. 6:475-482.
8. Chang S, Puryear J, Cairney J. 1993. A simple and efficient method for isolating RNA from pine trees. Plant Mol. Biol. Rep. 11:113-116.
9. Cullen DW, Hirsch PR. 1998. Simple and rapid method for direct extraction of microbial DNA from soil for PCR. Soil Biol. Biochem. 30:983-993.
10. Dell'Anno A, Fabiano M, Duineveld GCA, Kok A, Danovaro R. 1998. Nucleic acid (DNA, RNA) quantification and RNA/DNA ratio determination in marine sediments: Comparison of spectrophotometric, fluorometric, and high performance liquid chromatography methods and estimation of detrital DNA. Appl. Environ. Microbiol. 64:3238-3245.
11. Desai C, Madamwar D. 2007. Extraction of inhibitor-free metagenomic DNA from polluted sediments, compatible with molecular diversity analysis using adsorption and ion-exchange treatments. Bioresour. Technol. 98:761-768.
12. Dong D, Yan A, Liu, H, Zhang X, Xu Y. 2006. Removal of humic substances from soil DNA using aluminium sulfate. J. Microbiol. Methods 66:217-222.
13. Erb RW, Wagner-Dobler I. 1993. Detection of polychlorinated biphenyl degradation genes in polluted sediments by direct DNA extraction and polymerase chain reaction. Appl. Environ. Microbiol. 59:4065-4073.
14. Felske A, Engelen B, Nubel U, Backhaus H. 1996. Direct ribosome isolation from soil to extract bacterial rRNA for community analysis. Appl. Environ. Microbiol. 62:4162-4167.
15. Fleming JT, Yao WH, Sayler GS. 1998. Optimization of differential display of prokaryotic mRNA: Application to pure culture and soil microcosms. Appl. Environ. Microbiol. 64:3698-3706.
16. Fortin N, Beaumier D, Lee K, Greer CW. 2004. Soil washing improves the recovery of total community DNA from polluted and high organic content sediments. J. Microbiol. Methods 56:181-191.
17. Frostega°rd A, Courtois S, Ramisse V, Clerc S, Bernillon D, et al. 1999. Quantification of bias related to the extraction of DNA directly from soils. Appl. Environ. Microbiol. 65:5409-5420.
18. Gilbert JA, Field D, Huang Y, Edwards R, Li W, Gilna P, Joint I. 2008. Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. PLoS ONE 3(8):e3042.
19. Gich F, Schubert K, Bruns A, Hoffelner H, Overmann J. 2005. Specific detection, isolation, and characterization of selected, previously uncultured members of the freshwater bacterioplankton community. Appl. Environ. Microbiol. 71:5908-5919.
20. Gray JP, Herwig RP. 1996. Phylogenetic analysis of the bacterial communities in marine sediments. Appl. Environ. Microbiol. 62:4049-4059.
21. 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.
22. Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM. 1998. Molecular biological access to the chemistry of unknown soil microbes: A new frontier for natural products. Chem. Biol 5:245-249.
23. Harry M, Gambier B, Bourezgui Y, Garnier-Sillam E. 1999. Evaluation of purification procedures for DNA extracted from organic rich samples: interference with humic substances. Analysis 27:439-442.
24. He Z, Gentry TJ, Schadt CW, Wu L, Liebich J, et al. 2007. GeoChip: A comprehensive microarray for investigating biogeochemical, ecological, and environmental processes. ISME J. 1:67-77.
25. Holben WE, Jansson JK, Chelm BK, Tiedje JM. 1988. DNA probe method for the detection of specific microorganisms in the soil bacterial community. Appl. Environ. Microbiol. 54:703-711.
26. Howeler M, Ghiorse WC, Walker LP. 2003. A quantitative analysis of DNA extraction and purification from compost. J. Microbiol. Methods 54:37-45.
27. Hurt RA, Qiu X, Wu L, Roh Y, Palumbo AV, Tiedje AM, Zhou J. 2001. Simultaneous recovery of RNA and DNA from soils and sediments. Appl. Environ. Microbiol. 67:4495-4503.
28. Jacobsen CS, Rasmussen OF. 1992. Development and application of a new method to extract bacterial DNA from soil based on separation of bacteria from soil with cation-exchange resin. Appl. Environ. Microbiol. 58:2458-2462.
29. Jones BV, Marchesi J. 2007. Accessing the mobile metagenome of the human gut microbiota. Mol. Biosyst. 3:749-758.
30. Kerkhof L, Ward BB. 1993. Comparison of nucleic acid hybridization and fluorimetry for measurement of the relationship between RNA/DNA ratio and growth rate in a marine bacterium. Appl. Environ. Microbiol. 59:1303-1309.
31. Lakay FM, Botha A, Prior BA. 2007. Comparative analysis of environmental DNA extraction and purification methods from different humic acid-rich soils. J. Appl. Microbiol. 102:265-273.
32. La Montagne MG, Michel FC Jr, Holden PA, Reddy CA. 2002. Evaluation of extraction and purification methods for obtaining PCRamplifiable DNA from compost for microbial community analysis. J. Microbiol. Methods 49:255-264.
33. Lee SY, Bollinger J, Bezdicek D, Ogram A. 1996. Estimation of the abundance of an uncultured soil bacterial strain by a competitive quantitative PCR method. Appl. Environ. Microbiol. 62:3787-3793.
34. Leff LG, Dana JR, McArthur JV, Shimkets LJ. 1995. Comparison of methods of DNA extraction from stream sediments. Appl. Environ. Microbiol. 61:1141-1143.
35. Leininger S, Urich T, Schloter M, Schwark L, Qi J. 2006. Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442:806-809.
36. Lloyd-Jones G, Hunter DWF. 2001. Comparison of rapid DNA extraction methods applied to contrasting New Zealand soils. Soil Biol. Biochem. 33:2053-2059.
37. Loy A, Lehner A, Lee N, Adamczyk J, Meier H, et al. 2000. Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment. Appl. Environ. Microbiol. 68:5064-5081.
38. MacNeil IA, Tiong CL, Minor C, August PR, Grossman TH, et al. 2001. Expression and isolation of antimicrobial small molecules from soil DNA libraries. J. Mol. Microbiol. Biotechnol. 3(2): 301-308.
39. Miller DN, Bryant JE, Madsen EL, Ghiorse WC. 1999. Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples. Appl. Environ. Microbiol. 65:4715-4724.
40. Miller DN. 2001. Evaluation of gel filtration resins for the removal of PCR-inhibitory substances from soils and sediments. J. Microbiol. Methods 44:49-58.
41. Moran MA, Torsvik VL, Torsvik T, Hodso RE. 1993. Direct extraction and purification of rRNA for ecological studies. Appl. Environ. Microbiol. 59:915-918.
42. Moreira D. 1998. Efficient removal of PCR inhibitors using agarose embedded DNA preparations. Nucleic Acids Res. 26:3309-3310.
43. Moritz EM, Hergenrother PJ. 2007. Toxin-antitoxin systems are ubiquitous and plasmid-encoded in vancomycin-resistant enterococci. Proc. Natl. Acad. Sci. USA 104:311-316.
44. Muttray AF, Mohn WW. 2000. Quantitation of the population size and metabolic activity of a resin acid degrading bacterium in activated sludge using slot-blot hybridization to measure the rRNA:rDNA ratio. Microb. Ecol. 38:348-357.
45. Nannipieri P. 2006. Role of Stabilised Enzymes in Microbial Ecology and Enzyme Extraction from Soil with Potential Applications in Soil Proteomics, 1st ed. Berlin: Springer. Ogram A, Sayler GS, Barkay T. 1987. The extraction and purification of microbial DNA from sediments. J. Microbiol. Methods 7:57-66.
46. Ogunseitan OA. 2006. Soil Proteomics: Extraction and Analysis of Proteins from Soils, 1st ed. Berlin: Springer. Orsini M, Romano-Spica V. 2001. A microwave-based method for nucleic acid isolation from environmental samples. Lett. Appl. Microbiol. 33:17-20.
47. Parro V, Moreno-Paz M, Gonzalez-Toril E. 2007. Analysis of environmental transcriptomes by DNA microarrays. Environ. Microbiol. 9:453-464.
48. Picard C, Ponsonnet C, Paget E, Nesme X, Simonet P. 1992. Detection and enumeration of bacteria in soil by direct DNA extraction and polymerase chain reaction. Appl. Environ. Microbiol. 58:2717-2722.
49. Poretsky RS, Bano N, Buchan A, LeCleir G, Kleikemper J. 2005 Analysis of microbial gene transcripts in environmental samples. Appl. Environ. Microbiol. 71:4121-4126.
50. Porteous LA, Seidler RJ, Watrud LS. 1997. An improved method for purifying DNA from soil for polymerase chain reaction amplification and molecular ecology applications. Mol. Ecol. 6:787-791.
51. Purdy KJ, Embley TM, Takii S, Nedwell DB. 1996. Rapid extraction of DNA and rRNA from sediments by a novel hydroxyapatite spincolumn method. Appl. Environ. Microbiol. 62:3905-3907.
52. Radajewski S, Murrell JC. 2002. Stable-isotope probing for detection of methanotrophs after enrichment with 13CH4. Methods Mol. Biol. 179:149-157.
53. Rajendhran J, Gunasekaran P. 2008. Strategies for accessing soil metagenome for desired applications. Biotech. Adv. 26:576-590.
54. Ramsay AJ. 1984. Extraction of bacteria from soil: Efficiency of shaking or ultrasonication as indicated by direct counts and autoradiography. Soil Biol. Biochem. 16:475-481.
55. Riesenfeld CS, Schloss PD, Handelsman J. 2004. Metagenomics: Genomic analysis of microbial communities. Annu. Rev. Genet. 38:525-552.
56. Robe P, Nalin R, Capellano C, Vogel TM, Simonet P. 2003. Extraction of DNA from soil. Eur. J. Soil Biol. 39:183-190.
57. Rojas-Herrera R, Narváez-Zapata J, Zamudio-Maya M, Mena-Martínez ME. 2008. A simple silica-based method for metagenomic DNA extraction from soil and sediments. Mol. Biotechnol. 40:13-17.
58. Roose-Amsaleg CL, Garnier-Sillam E, Harry M. 2001. Extraction and purification of microbial DNA from soil and sediment samples. Appl. Soil. Ecol. 18:47-60.
59. Sandaa RA, Enger O, Torsvik V. 1998. Rapid method for fluorometric quantification of DNA in soil. Soil Biol. Biochem. 30:265-268.
60. Schwarz S, Waschkowitz T, Daniel R. 2005. Enhancement of gene detection frequencies by combining DNA-based stable-isotope probing with the construction of metagenomic DNA libraries. World J. Microbiol. Biotechnol. 22:363-368.
61. Senesi N, Loffredo E. 2001. Soil humic substances. In Hofrichter M, Steinbuchel A, eds. Biopolymers. Lignin, Humic Substances and Coal, Vol 1. Weinheim, Germany: Wiley-VCH, pp. 247-299.
62. Sessitsch A, Gyamfi S, Strails-Pavese N, Weilharter A, Pfeifer U. 2002. RNA isolation from soil for bacterial community and functional analysis: Evaluation of different extraction and soil conservation protocols. J. Microbiol. Methods 51:171-179.
63. Shendure J, Ji H. 2008. Next-generation DNA sequencing. Nat. Biotechnol. 26:1135-1145.
64. Spits C, Le Caignec C, De Rycke M, Van Haute L, Van Steirteghem A, et al. 2006. Optimization and evaluation of singlecell whole-genome multiple displacement amplification. Hum. Mutat. 27:496-503.
65. Steffan RJ, Goksoyr J, Bej AB, Atlas RM. 1988. Recovery of DNA from soils and sediments. Appl. Environ. Microbiol. 54:2908-2915.
66. Suzuki MT, Preston CM, Beja O, de la Torre JR, Steward GF, DeLong EF. 2004. Phylogenetic screening of ribosomal RNA genecontaining clones in bacterial artificial chromosome (BAC) libraries from different depths in Monterey Bay. Microb. Ecol. 48:473-488.
67. Tien CC, Chao CC, Chao WL. 1999. Methods for DNA extraction from various soils: A comparison. J. Appl. Microbiol. 86:937-943.
68. Tsai Y, Olson BH. 1991. Rapid method for direct extraction of DNA from soil and sediments. Appl. Environ. Microbiol. 57:1070-1074.
69. Urich T, Lanzen A, Qi J, Huson DH, Schleper C. 2008. Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome. PLoS ONE 3:e2527.
70. Volossiouk T, Robb EJ, Nazar RN. 1995. Direct DNA extraction for PCR-mediated assays of soil organisms. Appl. Environ. Microbiol. 61:3972-3976.
71. Widmer F, Seidler RJ, Gillevet PM, Watrud LS, Giovanni GD. 1998. A highly selective PCR protocol for detecting 16S rRNA genes of the genus Pseudomonas (sensu stricto) in environmental samples. Appl. Environ. Microbiol. 1998; 64:2545-2553.
72. Yeates C, M. Gillings MR, Davison AD, Altavilla N, Veal DA. 1997. Biol. Procedures Online 1:41-47.
73. Zhang L, Xu, Z, Bharat KCP. 2009. An improved method for purifying genomic DNA from forest leaf litters and soil suitable for PCR. J. Soils Sediments 9:261-266.
74. Zhou J, Bruns MA, Tiedje JM. 1996. DNA recovery from soils of diverse composition. Appl. Environ. Microbiol. 62:316-322.