DNA isolation from mud/soil

James Herrick jherrick at lanl.gov
Mon Oct 20 11:57:27 EST 1997

In article <pjc-1310971402170001 at>, pjc at waikato.ac.nz
(Peter J Charlton) wrote:

> Hi - I've been looking for a method of extracting PCR-able genomic DNA
> from sediments such as lake mud.  The trouble is, there are a lot of methods
> detailed in the literature, and nearly every author claims his/her method is
> the best.
> Would anyone like to tell me their favourite method and why?  or perhaps
> point me in the direction of a recent review of soil extraction methods?
> Many thanks,
> Peter.
> pjc at waikato.ac.nz

Well, I'm about to tell you that ours is the best! No, really, there are a
lot of good methods out there and they seem to be converging. We published
one of the first methods specifically for extracting DNA from *native*
bacteria (as opposed to those added in; a significant hurdle, we found) in
sediments and soil (Herrick et al. 1993. Appl. Environ. Microbiol.
59:687). Since that time we have modified the method somewhat and
successfully tested it on some of the nastiest, organic-rich sediments we
could find, looking at the same time at the efficiency of lysis of the
native cells (More' et al. 1994. AEM 60: 1572-1580). The most up-to-date
published version of this method is in an excellent little book called
'PCR:Essential Techniques', edited by Julian F. Burke (1996. Bios Sci.
Publ., Oxford). I can also send you a fuller version of this protocol via
e-mail, if you wish.

I like our method because it's versatile, reproducible, very fast, and
it's been used successfully in a lot of labs. The one drawback is that it
requires a beadbeater for physical lysis of cells.

Jim Herrick
Los Alamos National Laboratory
jherrick at lanl.gov

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