Logo of aemPermissionsJournals.ASM.orgJournalAEM ArticleJournal InfoAuthorsReviewers
Appl Environ Microbiol. Apr 1991; 57(4): 1070–1074.
PMCID: PMC182847

Rapid method for direct extraction of DNA from soil and sediments.


A rapid method for the direct extraction of DNA from soil and sediments was developed. The indigenous microorganisms in the soil and sediments were lysed by using lysozyme and a freeze-thaw procedure. The lysate was extracted with sodium dodecyl sulfate and phenol-chloroform. In addition to a high recovery efficiency (greater than 90%), the yields of DNA were high (38 and 12 micrograms/g [wet weight] from sediments and soil, respectively). This method generated minimal shearing of the extracted DNA. The crude DNA could be further purified with an Elutip-d column if necessary. An additional advantage of this method is that only 1 g of sample is required, which allows for the analysis of small samples and the processing of many samples in a relatively short (7 h) period.

Full text

Full text is available as a scanned copy of the original print version. Get a printable copy (PDF file) of the complete article (1.5M), or click on a page image below to browse page by page. Links to PubMed are also available for Selected References.

Images in this article

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Deflaun MF, Paul JH, Davis D. Simplified method for dissolved DNA determination in aquatic environments. Appl Environ Microbiol. 1986 Oct;52(4):654–659. [PMC free article] [PubMed]
  • Ferguson RL, Buckley EN, Palumbo AV. Response of marine bacterioplankton to differential filtration and confinement. Appl Environ Microbiol. 1984 Jan;47(1):49–55. [PMC free article] [PubMed]
  • Francisco DE, Mah RA, Rabin AC. Acridine orange-epifluorescence technique for counting bacteria in natural waters. Trans Am Microsc Soc. 1973 Jul;92(3):416–421. [PubMed]
  • Fuhrman JA, Comeau DE, Hagström A, Chan AM. Extraction from natural planktonic microorganisms of DNA suitable for molecular biological studies. Appl Environ Microbiol. 1988 Jun;54(6):1426–1429. [PMC free article] [PubMed]
  • Hobbie JE, Daley RJ, Jasper S. Use of nuclepore filters for counting bacteria by fluorescence microscopy. Appl Environ Microbiol. 1977 May;33(5):1225–1228. [PMC free article] [PubMed]
  • Holben William E, Jansson Janet K, Chelm Barry K, Tiedje James M. DNA Probe Method for the Detection of Specific Microorganisms in the Soil Bacterial Community. Appl Environ Microbiol. 1988 Mar;54(3):703–711. [PMC free article] [PubMed]
  • Jansson JK, Holben WE, Tiedje JM. Detection in soil of a deletion in an engineered DNA sequence by using DNA probes. Appl Environ Microbiol. 1989 Nov;55(11):3022–3025. [PMC free article] [PubMed]
  • Paul JH, Myers B. Fluorometric determination of DNA in aquatic microorganisms by use of hoechst 33258. Appl Environ Microbiol. 1982 Jun;43(6):1393–1399. [PMC free article] [PubMed]
  • Roszak DB, Colwell RR. Survival strategies of bacteria in the natural environment. Microbiol Rev. 1987 Sep;51(3):365–379. [PMC free article] [PubMed]
  • Sayler GS, Shields MS, Tedford ET, Breen A, Hooper SW, Sirotkin KM, Davis JW. Application of DNA-DNA colony hybridization to the detection of catabolic genotypes in environmental samples. Appl Environ Microbiol. 1985 May;49(5):1295–1303. [PMC free article] [PubMed]
  • Somerville CC, Knight IT, Straube WL, Colwell RR. Simple, rapid method for direct isolation of nucleic acids from aquatic environments. Appl Environ Microbiol. 1989 Mar;55(3):548–554. [PMC free article] [PubMed]
  • Steffan RJ, Goksøyr J, Bej AK, Atlas RM. Recovery of DNA from soils and sediments. Appl Environ Microbiol. 1988 Dec;54(12):2908–2915. [PMC free article] [PubMed]
  • Torsvik V, Goksøyr J, Daae FL. High diversity in DNA of soil bacteria. Appl Environ Microbiol. 1990 Mar;56(3):782–787. [PMC free article] [PubMed]
  • Torsvik V, Salte K, Sørheim R, Goksøyr J. Comparison of phenotypic diversity and DNA heterogeneity in a population of soil bacteria. Appl Environ Microbiol. 1990 Mar;56(3):776–781. [PMC free article] [PubMed]
  • Tsai YL, Olson BH. Effects of Hg, CH(3)-Hg, and Temperature on the Expression of Mercury Resistance Genes in Environmental Bacteria. Appl Environ Microbiol. 1990 Nov;56(11):3266–3272. [PMC free article] [PubMed]
  • Walia S, Khan A, Rosenthal N. Construction and applications of DNA probes for detection of polychlorinated biphenyl-degrading genotypes in toxic organic-contaminated soil environments. Appl Environ Microbiol. 1990 Jan;56(1):254–259. [PMC free article] [PubMed]

Articles from Applied and Environmental Microbiology are provided here courtesy of American Society for Microbiology (ASM)


Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...


  • Cited in Books
    Cited in Books
    PubMed Central articles cited in books
  • MedGen
    Related information in MedGen
  • PubMed
    PubMed citations for these articles
  • Substance
    PubChem Substance links

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...