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Preparation of Nucleic Acids from Marine Samples: Applications to Microbial Ecology Research

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Sample Preparation Techniques for Soil, Plant, and Animal Samples

Part of the book series: Springer Protocols Handbooks ((SPH))

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Abstract

The implementation of molecular techniques, and more recently the rise of metagenomic studies applied in marine systems, has revolutionized our understanding of marine ecology, especially in microbial research. Preparation of high-quality, representative, nucleic acids from cultures and raw marine samples is the basis of all molecular approaches. Presently, many protocols are available throughout the scientific literature but due to the vast diversity of marine environments and organisms, none of them could be used as a universal protocol that can fit for all marine samples (seawater as well as sediments). The purpose of this chapter is to highlight the key points involved in the preparation of nucleic acids from marine microbial communities, from sampling to extraction. A special attention is paid to the specific challenges faced in the marine environment.

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References

  1. Massana R (2011) Eukaryotic picoplankton in surface oceans. Annu Rev Microbiol 65:91–110

    Article  CAS  PubMed  Google Scholar 

  2. Pedrós-Alió C (2006) Genomics and marine microbial ecology. Int Microbiol 9:191–197

    PubMed  Google Scholar 

  3. Ganesh S, Parris DJ, DeLong EF et al (2014) Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone. ISME J 8:187–211

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  4. Gilbert JA, Dupont CL (2011) Microbial metagenomics : beyond the genome. Ann Rev Mar Sci 3:347–371

    Article  PubMed  Google Scholar 

  5. Iverson V, Morris RM, Frazar CD et al (2012) Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota. Science 335:587–590

    Article  CAS  PubMed  Google Scholar 

  6. Kennedy J, Flemer B, Jackson SA et al (2010) Marine metagenomics: new tools for the study and exploitation of marine microbial metabolism. Mar Drugs 8:608–628

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  7. Simon C, Daniel R (2011) Metagenomic analyses: past and future trends. Appl Environ Microbiol 77:1153–1161

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  8. Wilson IG (1997) Inhibition and facilitation of nucleic acid amplification. Appl Environ Microbiol 63:3741–3751

    PubMed Central  CAS  PubMed  Google Scholar 

  9. Van der Kraan GM, De Ridder M, Lomans BP, Muyzer G (2011) Sampling and nucleic extraction procedures from oil reservoir samples. In: Whitby C, Skovhus TL (eds) Applied microbiology and molecular biology in oilfield systems. Springer, New York

    Google Scholar 

  10. Paul JH (2004) Extraction of microbial DNA from aquatic sources: marine environments. In: Kowalchuk GA, de Bruijn FJ, Head IM, Akkermans ADL, van Elsas JD (eds) Molecular microbial ecology manual, vol 1, 2nd edn. Kluwer Academic, The Netherlands, pp 29–40

    Google Scholar 

  11. Fuhrman JA, Comeau DE, Hagstrom A et al (1988) Extraction from natural planktonic microorganisms of DNA suitable for molecular biological studies. Appl Environ Microbiol 54:1426–1429

    PubMed Central  CAS  PubMed  Google Scholar 

  12. Ferguson RL, Buckley EN, Palumbo AV (1984) Response of marine bacterioplankton to differential filtration and confinement. Appl Environ Microbiol 47:49–55

    PubMed Central  CAS  PubMed  Google Scholar 

  13. Diez B, Pedros-Alio C, Massana R (2001) Study of genetic diversity of eukaryotic picoplankton in different oceanic regions by small subunit rRNA gene cloning and sequencing. Appl Environ Microbiol 67:2932–2941

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  14. Sommerville CC, Knight IT, Straube WL et al (1989) Simple, rapid method for direct isolation of nucleic acids form aquatic environments. Appl Environ Microbiol 55:548–554

    Google Scholar 

  15. Urakawa H, Martens-Habbena W, Stahl DA (2010) High abundance of ammonia-oxidizing Archaea in coastal waters, determined using a modified DNA extraction method. Appl Environ Microbiol 76:2129–2135

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  16. Wright JJ, Lee S, Zaikova E et al. (2009) DNA extraction from 0.22 μM Sterivex filters and cesium chloride density gradient centrifugation. J Vis Exp (31). doi: 10.3791/1352

  17. Gast RJ, Dennett MR, Caron DA (2004) Characterization of protistan assemblages in the Ross sea, Antarctica, by denaturant gradient gel electrophoresis. Appl Environ Microbiol 70:2028–2037

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  18. Giovannoni SJ, DeLong EF, Schmidt TM et al (1990) Tangential flow filtration and preliminary phylogenetic analysis of marine picoplankton. Appl Environ Microbiol 56:2572–2575

    PubMed Central  CAS  PubMed  Google Scholar 

  19. DeLong EF, Franks DG, Alldredge AL (1993) Phylogenetic diversity of aggregate-attached vs free-living marine bacterial assemblages. Limnol Oceanogr 38:924–934

    Article  Google Scholar 

  20. Boehme J, Frischer ME, Jiang SC et al (1993) Viruses, bacterioplankton and phytoplankton in the southeastern gulf of Mexico: distribution and contribution to oceanic DNA pools. Mar Ecol Prog Ser 97:1–10

    Article  Google Scholar 

  21. Jiang SC, Thurmond JM, Pichard SL et al (1992) Concentration of microbial populations from aquatic environments by vortex flow filtration. Mar Ecol Prog Ser 80:101–107

    Article  Google Scholar 

  22. Taylor GI (1923) Stability of a viscous liquid contained between two rotating cylinders. Phil Trans R Soc London 223:289–343

    Article  Google Scholar 

  23. Paul JH, Jiang SC, Rose JB (1991) Concentration of viruses and dissolved DNA from aquatic environments by vortex flow filtration. Appl Environ Microbiol 57:2197–2204

    PubMed Central  CAS  PubMed  Google Scholar 

  24. Smith CM, Hill VR (2009) Dead end hollow fiber ultrafiltration for recovery of diverse microbes from water. Appl Environ Microbiol 75:5284–5289

    Article  PubMed Central  PubMed  Google Scholar 

  25. Kearns EA, Magana S, Lim DV (2008) Automated concentration and recovery of micro-organisms from drinking water using dead end ultrafiltration. J Appl Microbiol 105:432–442

    Article  CAS  PubMed  Google Scholar 

  26. Leskinen SD, Lim DV (2008) Rapid ultrafiltration concentration and biosensor detection of Enterococci from large volumes of Florida recreational water. Appl Environ Microbiol 74:4792–4798

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  27. Leskinen SD, Kearns EA, Jones WL et al (2012) Automated dead end ultrafiltration of large volume water samples to enable detection of low level targets and reduce sample variability. J Appl Microbiol 113:351–360

    Article  CAS  PubMed  Google Scholar 

  28. Hurt RA, Qiu X, Wu L et al (2001) Simultaneous recovery of RNA and DNA from soils and sediments. Appl Environ Microbiol 67:4495–4503

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  29. Luna GM, Dell’Anno A, Danovaro R (2006) DNA extraction procedure: a critical issue for bacterial diversity assessment in marine sediments. Environ Microbiol 8:308–320

    Article  CAS  PubMed  Google Scholar 

  30. Faegri A, Torsvik VL, Goksor J (1977) Bacterial and fungial activities in soil: separation of bacteria and fungi by a rapid fractionated centrifugation technique. Soil Biol Biochem 9:105–112

    Article  Google Scholar 

  31. Bettarel Y, Bouvy M, Dumont C et al (2006) Virus-bacterium interactions in water and sediment of West African inland aquatic systems. Appl Environ Microbiol 72:5274–5282

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  32. Danovaro R, Dell’Anno A, Trucco A et al (2001) Determination of virus abundance in marine sediment. Appl Environ Microbiol 67:1384–1387

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  33. Velji MI, Albright LJ (1986) Microscopic enumeration of attached marine bacteria of seawater, marine sediment, fecal matter, and kelp blade samples following pyro- phosphate and ultrasound treatments. Can J Microbiol 32:121–126

    Article  Google Scholar 

  34. 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

    Article  Google Scholar 

  35. Lindahl T (1993) Instability and decay of the primary structure of DNA. Nature 362:709–715

    Article  CAS  PubMed  Google Scholar 

  36. Rossmanith P, Roder B, Fruhwirth K et al (2011) Mechanisms of degradation of DNA standards for calibration function during storage. Appl Microbiol Biotechnol 89:407–417

    Article  CAS  PubMed  Google Scholar 

  37. Rochelle PA, Cragg BA, Fry JC et al (1994) Effect of sample handling on estimation of bacterial diversity in marine sediments by 16S rRNA gene sequence analysis. FEMS Microbiol Ecol 15:215–226

    Article  CAS  Google Scholar 

  38. Dorigo U, Fontvieille D, Humbert JF (2006) Spatial variability in the abundance and composition of the free-living bacterioplankton community in the pelagic zone of the Lake Bourget (France). FEMS Microbiol Ecol 58:109–119

    Article  CAS  PubMed  Google Scholar 

  39. Gray MA, Pratte ZA, Kellogg CA (2013) Comparison of DNA preservation methods for environmental bacterial community samples. Microb Ecol 83:468–477

    Article  CAS  Google Scholar 

  40. Picard C, Ponsonnet C, Paget E et al (1992) Detection and enumeration of bacteria in soil by direct DNA extraction and polymerase chain reaction. Appl Environ Microbiol 58:2717–2722

    PubMed Central  CAS  PubMed  Google Scholar 

  41. Massana R, Murray AE, Preston CM et al (1997) Vertical distribution and phylogenetic characterization of marine planktonic Archaea in the Santa Barbara channel. Appl Environ Microbiol 63:50–56

    PubMed Central  CAS  PubMed  Google Scholar 

  42. Schmidt TM, DeLong EF, Pace NR (1991) Analysis of marine picoplankton community by 16S rRNA gene cloning and sequencing. J Bacteriol 173:4371–4378

    PubMed Central  CAS  PubMed  Google Scholar 

  43. Miller DN, Bryant JE, Madsen EL et al (1999) Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples. Appl Environ Microbiol 65:4715–4724

    PubMed Central  CAS  PubMed  Google Scholar 

  44. Moré MI, Heerrick JB, Silva MC et al (1994) Quantitative cell lysis of indigenous microorganisms and rapid extraction of microbial DNA from sediment. Appl Environ Microbiol 60:1572–1580

    PubMed Central  PubMed  Google Scholar 

  45. Cox AM, Goodwin KD (2013) Sample preparation methods for quantitative detection of DNA by molecular assays and marine biosensors. Mar Poll Bull 73:47–56

    Article  CAS  Google Scholar 

  46. Biddle JF, Lipp JS, Lever MA et al (2006) Heterotrophic archaea dominate sedimentary subsurface ecosystems off Peru. Proc Natl Acad Sci U S A 103:3846–3851

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  47. Kim B-H, Ramanan R, Cho D-H, Choi G-G, La H-J et al (2012) Simple, rapid and cost-effective method for high quality nucleic acids extraction from different strains of Botryococcus braunii. PLoS ONE 7(5), e37770

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  48. Lloyd KG, MacGregor BJ, Teske A (2010) Quantitative PCR methods for RNA and DNA in marine sediments: maximizing yield while overcoming inhibition. FEMS Microbiol Ecol 72:143–151

    Article  CAS  PubMed  Google Scholar 

  49. Eland LE, Davenport R, Mota CR (2012) Evaluation of DNA extraction methods for freshwater eukaryotic microalgae. Water Res 46:5355–5364

    Article  CAS  PubMed  Google Scholar 

  50. Simonelli P, Troedsson C, Nejstgaard JC et al (2009) Evaluation of DNA extraction and handling procedures for PCR-based copepod feeding studies. J Plankton Res 31:1465–1474

    Article  CAS  Google Scholar 

  51. Inagaki F, Nunoura T, Nakagawa S et al (2006) Biogeographical distribution and diversity of microbes in methane hydratebearing deep marine sediments on the Pacific Ocean Margin. Proc Natl Acad Sci U S A 103:2815–2820

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  52. Sørensen KB, Lauer A, Teske A (2004) Archaeal phylotypes in a metal-rich and low-activity deep subsurface sediment of the Peru Basin, ODP Leg 201, site 1231. Geobiology 2:151–161

    Article  Google Scholar 

  53. Whitehouse CA, Hottel HE (2007) Comparison of five commercial DNA extraction kits for the recovery of Francisella tularensis DNA from spiked soil samples. Mol Cell Probes 21:92–96

    Article  CAS  PubMed  Google Scholar 

  54. Alain K, Callac N, Ciobanu MC et al (2011) DNA extraction from deep subseafloor sediments: novel cryogenic-mill-based procedure and comparison to existing protocols. J Microbiol Methods 87:355–362

    Article  CAS  PubMed  Google Scholar 

  55. Ottesen EA, Marin R III, Preston CM et al (2011) Metatranscriptomic analysis of autonomously collected and preserved marine bacterioplankton. ISME J 5:1881–1895

    Article  PubMed Central  CAS  PubMed  Google Scholar 

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Author information

Authors and Affiliations

  1. Institut des sciences de la mer de Rimouski (ISMER), Université du Québec à Rimouski, 310 allée des Ursulines, Rimouski, QC, Canada

    Karine Lemarchand Ph.D. & Thomas Pollet Ph.D.

  2. Department of Molecular Biology, Centre de recherche sur les biotechnologies marines (CRBM), 265, 2e Rue Est, Rimouski, QC, Canada

    Vincent Lessard M.S. & M. Amine Badri Ph.D.

Authors
  1. Karine Lemarchand Ph.D.
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  2. Thomas Pollet Ph.D.
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  3. Vincent Lessard M.S.
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  4. M. Amine Badri Ph.D.
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Corresponding author

Correspondence to Karine Lemarchand Ph.D. .

Editor information

Editors and Affiliations

  1. Department of Engineering Design Technology, Cerritos College, Norwalk, California, USA

    Miodrag Micic

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Lemarchand, K., Pollet, T., Lessard, V., Badri, M.A. (2016). Preparation of Nucleic Acids from Marine Samples: Applications to Microbial Ecology Research. In: Micic, M. (eds) Sample Preparation Techniques for Soil, Plant, and Animal Samples. Springer Protocols Handbooks. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3185-9_23

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  • DOI: https://doi.org/10.1007/978-1-4939-3185-9_23

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-3184-2

  • Online ISBN: 978-1-4939-3185-9

  • eBook Packages: Springer Protocols

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