DNA isolation from mud/soil

Marcus Schmidt marcus.schmidt at tu-bs.de
Tue Oct 21 03:50:36 EST 1997

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

Gee, and I thought Ogram et al. (1988) had been the first. 

> 	   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.

An important paper of yours, and you have developed a fine method! I
agree with you in the absolute necessity of bead beating - part of my
experimental work had been devoted to the detection of Bacillus
endospores, and bead beating proved to be the only way to crack them up.

> 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.

It's not. No alternative published - so far, with the possible exemption
of sonification, which, however, shears the DNA even more. 

One thing that might be worth trying (I didn't do it) is the
PEG-precipitation of purified extracts (I used Wizard instead of
spin-bind, with not fully satisfactory results) suggested by Purdy et al
(1996, AEM 62(10):1905-7). If you did, or anybody else following the
discussion, please tell me. The method is cheap, available, and should
be able to effect additional humic acid removal.


     Marcus Schmidt
(marcus.schmidt at tu-bs.de)

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