Advertisement

Extraction of DNA and RNA from Aquatic Environments

  • J. H. Paul
  • S. L. Pichard
Part of the Springer Lab Manuals book series (SLM)

Abstract

The capability to work with nucleic acids isolated from mixed microbial communities from aquatic environments opens a new avenue of investigation for understanding the structure and function of aquatic microbial communities. These technologies have enabled microbial ecologists to answer questions that could not be answered by the classical isolation and cultivation approach to aquatic microbiology. In the first part of this chapter, we review literature on the extraction and quantitation of nucleic acids from aquatic environments as biomass indicators. In the second part we discuss extraction of nucleic acids (both dissolved and particulate) for molecular biological purposes and provide protocols that are useful for this purpose.

Keywords

Sodium Dodecyl Sulfate Aquatic Environment Viral Abundance Natural Microbial Community Guanidinium Isothiocyanate 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Adams RLP, Knowler JT, Leader DP (1986) The biochemistry of the nucleic acids, 10th ed. Chapman and Hall, New York, p 526CrossRefGoogle Scholar
  2. Bailiff MD, Karl DM (1991) Dissolved and particulate DNA dynamics during a spring bloom in the Antarctic Peninsula region, 1986-1987. Deep Sea Res 38: 1077–1095CrossRefGoogle Scholar
  3. Bateson MM, Wiegel J, Ward DM (1989) Comparative analysis of 16S ribosomal RNA sequences of thermophilic fermentative bacteria isolated from hot spring cyanobacterial mats. Syst Appl Microbiol 12: 1–7CrossRefGoogle Scholar
  4. Beebee TJC (1991) Analysis, purification and quantification of extracellular DNA from aquatic environments. Fresh Biol 25: 525–532CrossRefGoogle Scholar
  5. Berdalet E, Dortch Q (1991) New double-staining technique for RNA and DNA measurement in marine phytoplankton. Mar Ecol Prog Ser 73: 295–305CrossRefGoogle Scholar
  6. Bergh O, Borsheim KY, Bratbak G, Heldal M (1989) High abundance of viruses found in aquatic environments. Nature 340: 467–468CrossRefGoogle Scholar
  7. Boehme J, Friseher ME, Jiang SC, Kellogg CA, Pichard S, Rose JB, Steinway C, Paul JH (1993) Viruses, bacterioplankton, and phytoplankton in the southeastern Gulf of Mexico:distribution and contribution to oceanic DNA pools. Mar Ecol Progr Ser 97: 1–10CrossRefGoogle Scholar
  8. Brettar I, Hofle MG (1993) Nitrous oxide producing heterotrophic bacteria from the water column of the central Baltic: abundance and molecular identification. Mar Ecol Prog Ser 94: 253–265Google Scholar
  9. Costa-Pierce BA, Craven DB (1987) Estimating microbial production and growth rates in aquaculture ponds using rates of RNA and DNA synthesis. Aquaculture 66: 69–78CrossRefGoogle Scholar
  10. Craven DB, Karl DM (1984) Microbial RNA and DNA synthesis in marine sediments. Mar Biol 83: 129–139CrossRefGoogle Scholar
  11. DeFlaun MF, Paul JH, Davis D (1986) Simplified method for dissolved DNA determination in aquatic environments. Appl Environ Microbiol 52: 654–659Google Scholar
  12. DeFlaun MF, Paul JH, Jeffrey WH (1987) Distribution and molecular weight of dissolved DNA in subtropical estuarine and oceanic environments. Mar Ecol Progr Ser 38: 65–73CrossRefGoogle Scholar
  13. DeLong EF (1992) Archaea in coastal marine environments. Proc Natl Acad Sci USA 89: 5685–5689CrossRefGoogle Scholar
  14. de Madariaga I, Joint I (1992) A comparative study of phytoplankton physiological indicators. J Exp Mar Biol Ecol 158: 149–165CrossRefGoogle Scholar
  15. Dortch Q, Roberts TL, Clayton JR, Ahmed SI (1983) RNA to DNA ratios and DNA concentrations as indicators of growth rate and biomass in planktonic marine organisms. Mar Ecol Prog Ser 13: 61–71CrossRefGoogle Scholar
  16. Dortch Q, Clayton JR, Thoresen SS, Ahmed SI (1984) Species differences in accumulation of nitrogen pools in phytoplankton. Mar Biol 81: 237–250CrossRefGoogle Scholar
  17. Dortch Q, Clayton JR, Thoresen SS, Cleveland JS, Bressler SL, Ahmed SI (1985) Nitrogen storage and use of biochemical indices to assess nitrogen deficiency and growth rate in natural plankton populations. J Mar Res 43: 437–464CrossRefGoogle Scholar
  18. Farrell RE Jr (1993) RNA methodologies: a laboratory guide for isolation and characterization. Academic Press, San Diego p 317Google Scholar
  19. Francisco DE, Mah RA, Rabin AC (1973) Acridine orange epifluorescence technique for counting bacteria in natural waters. Trans Am Microsc Soc 92: 416–421CrossRefGoogle Scholar
  20. Fuhrman JE, Comeau DE, Hagstrom A, Chan AM (1988) Extraction from natural planktonic mieroorganismsm of DNA suitable for molecular biological studies. Appl Environ Microbiol 54: 1426–1429Google Scholar
  21. Giovannoni SJ, Britschgi TB, Moyer CL, Field KG (1990a) Genetic diversity in Sargasso Sea bacterioplankton. Nature 345: 60–63CrossRefGoogle Scholar
  22. Giovannoni SJ, DeLong EF, Schmidt TM, Pace NR (1990b) Tangential flow filtration and preliminary phylogenetic analysis of marine picoplankton. Appl Environ Microbiol 56: 2572–2575Google Scholar
  23. Guede H (1990) Bacterial net production approaching zero: a frequent phenomenon in pelagic environments. Ergeb Limnol 34: 165–169Google Scholar
  24. Guede H, Juergens K, Parth G, Walser R (1991) Indications for low net productivity of pelagic bacterioplankton. Kiel Meeresforsch 8: 309–316Google Scholar
  25. Hahn D, Kester R, Starrenburg MJC, Akkermans ADL (1990) Extraction of ribosomal RNA from soil for detection of Frankia with oligonucleotide probes. Arch Microbiol 154: 329–335CrossRefGoogle Scholar
  26. Hanson RB, Lowery HK (1983) Nucleic acid synthesis in oceanic mieroplankton from the Drake Passage, Antarctica: evaluation of steady-state growth. Mar Biol 73: 79–89CrossRefGoogle Scholar
  27. Hobbie JE, Daley RJ, Jasper S (1977) Use of Nuclepore filters for counting bacteria by fluorescence microscopy. Appl Environ Microbiol 33: 1225–1228Google Scholar
  28. Hofie MG (1988a) Identification of bacteria by low molecular weight RNA profiles: a new chemotaxonomic approach. J Microbiol Methods 8: 235–248CrossRefGoogle Scholar
  29. Hofle MG (1988b) Taxonomic structure of bacterial communities in mixed cultures as measured by low molecular weight RNA profiles. Ergeb Limnol 31: 71–77Google Scholar
  30. Hofle MG (1990a) Transfer RNAs as genotypic fingerprints of eubacteria. Arch Microbiol 153: 299–304CrossRefGoogle Scholar
  31. Hofle MG (1990b) RNA chemotaxonomy of bacterial isolates and natural microbial communities. In: Overbeck J, Chrost RJ (eds) Aquatic microbial ecology: biochemical and molecular approaches. Springer, Berlin, Heidelberg, New York, pp 129–159Google Scholar
  32. Hofle MG (1992) Bacterioplankton community structure and dynamics after large-scale release of nonindigenous bacteria as revealed by low-molecular-weight-RNA analysis. Appl Environ Microbiol 58: 3387–3394Google Scholar
  33. Hofle MG, Brettar I (1990) Correlation between microbial activity and taxonomic structure in the water column of the central Baltic. Ergeb Limnol 34: 237Google Scholar
  34. Holm-Hansen O (1969) Determination of microbial bioniass in ocean profiles. Limnol Oceanogr 14: 740–747CrossRefGoogle Scholar
  35. Holm-Hansen O, Sutcliffe Jr WH, Sharp J (1968) Measurement of deoxyribonucleic acid in the ocean and its ecological significance. Limnol Oceanogr 13: 507–514CrossRefGoogle Scholar
  36. Iwamura T, Kanazawa K, Shibata Y, Morimura S, Ichimura S, Maeda O, Tamiya H (1967) Preliminary studies on the feasibility of microanalytic measurement of planktonic populations. J Oceanog Soc Jpn 23: 247–251Google Scholar
  37. Jeffrey WH, Nazaret S, Von Haven R (1993) Improved method for extraction of mRNA form aquatic samples: application to detecting mer gene expression. General meeting of the American Society for Microbiology, Atlanta, USA (abstr N 29 )Google Scholar
  38. Jiang SC (1993) Viruses and the contribution of viral DNA to dissolved DNA in the marine environment. MSc Thesis, University of S Florida, Tampa, USAGoogle Scholar
  39. Jiang SC, Thurmond JM, Pichard SL, Paul JH (1992) Concentration of microbial populations from aquatic environments by vortex flow filtration. Mar Ecol Progr Ser 80: 101–107CrossRefGoogle Scholar
  40. Karl DM (1979) Measurement of microbial activity and growth in the ocean by rates of stable ribonucleic acid synthesis. Appl Environ Microbiol 38: 850–860Google Scholar
  41. Karl DM, Bailiff MG (1989) The measurement and distribution of dissolved nucleic acids in aquatic environments. Limnol Oceanogr 34: 543–558CrossRefGoogle Scholar
  42. Karl DM, Novitsky JA (1988) Dynamics of microbial growth in surface layers of a coastal marine sediment. Mar Ecol Progr Ser 50: 169–176Google Scholar
  43. Karl DM, Winn CD, Wong DCL (1981a) RNA synthesis as a measure of microbial growth in aquatic environments. I. Evaluation, verification, and optimization of methods. Mar Biol 64: 1–12Google Scholar
  44. Karl DM, Winn CD, Wong DCL (1981b) RNA synthesis as a measure of microbial growth in aquatic environments. II. Field applications. Mar Biol 64: 13–21Google Scholar
  45. Kemp PF, Lee S, LaRoche J (1993) Estimating the growth rate of slowly growing marine bacteria from RNA content. Appl Environ Microbiol 59: 2594–2601Google Scholar
  46. Kerkhof L, Ward BB (1993) Comparison of nucleic acid hybridization and fluorometry for measurement of the relationship between RNA to DNA ratio and growth rate in a marine bacterium. Appl Environ Microbiol 59: 1303–309Google Scholar
  47. Kissane JM, Robins E (1958) The fluorometric measurement of deoxyribonucleic acid in animal tissues with special reference to the central nervous system. J Biol Chem 233: 184–188Google Scholar
  48. Kjeldgaard NO (1967) Regulation of nucleic acid and protein synthesis in bacteria. Adv Mierob Physiol 1: 39–95CrossRefGoogle Scholar
  49. Knight IT, DiRuggiero J, Colwell RR (1991) Direct detection of enteropathogenic bacteria in estuarine water using nucleic acid probes. Water Sci Technol 24: 261–266Google Scholar
  50. Kramer JG, Singleton FL (1993) Measurement of rRNA variations in natural communities of microorganisms on the Southeastern U.S. continental shelf. Appl Environ Microbiol 59: 2430–2436Google Scholar
  51. Maniatis T, Fritsch EF, Sam brook J (1982) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory, Cold Spring HarborGoogle Scholar
  52. Marmur J (1961) A procedure for the isolation of deoxyribonucleic acid from microorganisms. J Mol Biol 3: 208–218CrossRefGoogle Scholar
  53. Maruyama A, Oda M, Higashihara T (1993) Abundance of virus-sized non-DNase-digestible DNA (coated DNA) in eutrophic sea water. Appl Environ Microbiol 59: 712–717Google Scholar
  54. Minear RA (1972) Characterization of naturally occurring dissolved organophosphorus componds. Environ Sci Technol 6: 431–437CrossRefGoogle Scholar
  55. Moran MA, Torsvik VL, Torsvik T, Hodson RE (1993) Direct extraction and purification of rRNA for ecological studies. Appl Environ Microbiol 59: 915–918Google Scholar
  56. Mordy CW, Carlson DJ (1991) An evaluation of fluorescence techniques for measuring DNA and RNA in marine microorganisms. Mar Ecol Prog Ser 73: 283–293CrossRefGoogle Scholar
  57. Nazaret S, Jeffrey WH, Von Haven R, Saouter E, Barkay T (1993) mer gene expression in aquatic environments. General meeting of the American Society for Microbiology, Atlanta, USA(abst N84 )Google Scholar
  58. Novitsky JA, Karl DM (1986) Characterization of microbial activity in the surface layers of a coastal sub-tropical sediment. Mar Ecol Prog Ser 28: 49–55CrossRefGoogle Scholar
  59. OgunScitan OA, Olson BH (1993) Effect of 2-hydroxybenzoate on the rate of naphthalene mineralization in soil. Appl Environ Microbiol 38: 799–807Google Scholar
  60. Paul JH, Carlson DJ (1984) Genetic material in the marine environment: implication for bacterial DNA. Limnol Oceanogr 29: 1091–1097CrossRefGoogle Scholar
  61. Paul JH, Cazares L, Thurmond J (1990a) Amplification of the rbcL gene from dissolved and particulate DNA from aquatic environments. Appl Environ Microbiol 56: 1963–1966Google Scholar
  62. Paul JH, Jeffrey WH, Cannon JP (1990b) Production of dissolved DNA, RNA, and protein by microbial populations in a Florida reservoir. Appl Environ Microbiol 56: 2957–2962Google Scholar
  63. Paul JH, Jeffrey WH, DeFlaun M (1985) Particulate DNA in subtropical oceanic and estuarine planktonie environments. Mar Biol 90: 95–101CrossRefGoogle Scholar
  64. Paul JH, Jeffrey WH, DeFlaun M (1987) Dynamics of extracellular DNA in the marine environment. Appl Environ Microbiol 53: 170–179Google Scholar
  65. Paul JH, Jiang SC, Rose JB (1991) Concentration of viruses and dissolved DNA from aquatic environments by vortex flow filtration. Appl Environ Microbiol 57: 2197–2204Google Scholar
  66. Paul JH, Myers B (1982) Fluorometric determination of DNA in aquatic microorganisms by use of Hoechst 33258. Appl Environ Microbiol 43: 1393–1399Google Scholar
  67. Piehard SL, Paul JH (1991) Detection of gene expression in genetically engineered microorganisms and natural phytoplankton populations in the marine environment by mRNA analysis. Appl Environ Microbiol 57: 1721–1727Google Scholar
  68. Piehard SL, Paul JH (1993) Gene expression per gene dose, a specific measure of gene expression in aquatic microorganisms. Appl Environ Microbiol 59: 451–457Google Scholar
  69. Pichard SL, Frischer ME, Paul JH (1993) Ribulose bisphosphate carboxylase gene expression in subtropical marine phytoplankton populations. Mar Ecol Prog Ser 101: 55–65CrossRefGoogle Scholar
  70. Pillai TNV, Ganguly AK (1970) Nucleic acids in the dissolved constituents of sea-water. Curr Sci 22: 501–504Google Scholar
  71. Pillai TNV, Ganguly AK (1972) Nucleic acids in the dissolved constituents of sea water. J Mar Biol Ass India 14: 384–390Google Scholar
  72. Proctor LM, Fuhrman JA (1990) Viral mortality of marine bacteria and cyanobacteria. Nature 343: 60–62CrossRefGoogle Scholar
  73. Rowan R, Powers DA (1992) Ribosomal RNA sequences and the diversity of symbiotic dinoflagellates (zooxanthellae). Proc Natl Acad Sci USA 89: 3639–3643CrossRefGoogle Scholar
  74. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn., Cold Spring Harbor Laboratory, Cold Spring HarborGoogle Scholar
  75. Selenska S, Klingmuller W (1994) Direct recovery and molecular analysis of DNA and RNA from Soil. Microb Rel (in press)Google Scholar
  76. Sommerville CC, Knight IT, Straube WL, Colwell RR (1989) Simple, rapid method for direct isolation of nucleic acids from aquatic environments. Appl Environ Microbiol 55: 548–554Google Scholar
  77. Suttle CA, Chan AM, Cottrell MT (1990) Infection of phytoplankton by viruses and reduction of primary productivity. Nature 347: 467–469CrossRefGoogle Scholar
  78. Suttle CA, Chan AM, Cottrell MT (1991) Use of ultrafiltration to isolate viruses from seawater which are pathogens of marine phytoplankton. Appl Environ Microbiol 57: 721–726Google Scholar
  79. Takahashi M, Nagai H, Yamaguchi Y Ichiniura S (1974) The distribution of chlorophyll a, protein, RNA and DNA in the North Pacific Ocean. J Oceanog Soc Japan 30: 137–150Google Scholar
  80. Tebbe CC, OgunScitan OA, Rochelle PA, Tsai YL, Olson BH (1992) Varied responses in gene expression of culturable heterotrophic bacteria isolated from the environment. Appl Microbiol Biotechnol 37: 818–824CrossRefGoogle Scholar
  81. Tougianidou D, Botzenhart K (1991) Detection of poliovirus in water by direct isolation of the RNA and hybridization with gene probes. Water Sci Technol 24: 273–276Google Scholar
  82. Tougianidou D, Botzenhart K (1993) Detection of enteroviral RNA sequences in different water samples. Water Sci Technol 27: 219–222Google Scholar
  83. Tsai YL, Olson BH (1990) Effects of Hg2+, CH3-Hg+, and temperature on the expression of mercury resistance genes in environmental bacteria. Appl Environ Microbiol 56: 3266–3272Google Scholar
  84. Tsai YL, Park MJ, Olson BH (1991) Rapid method for direct extraction of mRNA from seeded soils. Appl Environ Microbiol 57: 765–768Google Scholar
  85. Ward DM, Weller R, Bateson MM (1990) 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 345: 63–65Google Scholar
  86. Weller R, Ward DM (1989) Selective recovery of 16S rRNA sequences from natural microbial communities in the form of cDNA. Appl Environ Microbiol 55: 1818–1822Google Scholar
  87. Wells ML, Goldberg ED (1991) Occurrence of small colloids in sea water. Nature 353: 342–344CrossRefGoogle Scholar
  88. Wells ML, Goldberg ED (1993) Colloid aggregation in seawater. Mar Chem 41: 353–358CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 1995

Authors and Affiliations

  • J. H. Paul
  • S. L. Pichard

There are no affiliations available

Personalised recommendations